3KZI | pdb_00003kzi

Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II

PDB DOI: https://doi.org/10.2210/pdb3KZI/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Thermosynechococcus vestitus BP-1
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2009-12-08 Released: 2010-06-16
Deposition Author(s): Gabdulkhakov, A., Guskov, A., Broser, M., Kern, J., Zouni, A., Saenger, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.308 (Depositor), 0.303 (DCC)
R-Value Work:
0.297 (Depositor), 0.296 (DCC)
R-Value Observed:
0.297 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Monomeric Photosystem II from Thermosynechococcus elongatus at 3.6-A Resolution

Broser, M., Gabdulkhakov, A., Kern, J., Guskov, A., Muh, F., Saenger, W., Zouni, A.

(2010) J Biological Chem 285: 26255-26262

PubMed: 20558739 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M110.127589
Primary Citation Related Structures:
3KZI

PubMed Abstract:
The membrane-embedded photosystem II core complex (PSIIcc) uses light energy to oxidize water in photosynthesis. Information about the spatial structure of PSIIcc obtained from x-ray crystallography was so far derived from homodimeric PSIIcc of thermophilic cyanobacteria. Here, we report the first crystallization and structural analysis of the monomeric form of PSIIcc with high oxygen evolution capacity, isolated from Thermosynechococcus elongatus. The crystals belong to the space group C222(1), contain one monomer per asymmetric unit, and diffract to a resolution of 3.6 A. The x-ray diffraction pattern of the PSIIcc-monomer crystals exhibit less anisotropy (dependence of resolution on crystal orientation) compared with crystals of dimeric PSIIcc, and the packing of the molecules within the unit cell is different. In the monomer, 19 protein subunits, 35 chlorophylls, two pheophytins, the non-heme iron, the primary plastoquinone Q(A), two heme groups, 11 beta-carotenes, 22 lipids, seven detergent molecules, and the Mn(4)Ca cluster of the water oxidizing complex could be assigned analogous to the dimer. Based on the new structural information, the roles of lipids and protein subunits in dimer formation of PSIIcc are discussed. Due to the lack of non-crystallographic symmetry and the orientation of the membrane normal of PSIIcc perpendicular ( approximately 87 degrees ) to the crystallographic b-axis, further information about the structure of the Mn(4)Ca cluster is expected to become available from orientation-dependent spectroscopy on this new crystal form.

Organizational Affiliation

Institute of Chemistry, Max Volmer Laboratory of Biophysical Chemistry, Technische Universität Berlin, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 364.39 kDa
Atom Count: 24,678
Modeled Residue Count: 2,597
Deposited Residue Count: 2,714
Unique protein chains: 19

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem Q(B) protein 1	A	344	Thermosynechococcus vestitus BP-1	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A444 Go to UniProtKB: P0A444
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A444
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II core light harvesting protein	B	510	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIQ1 Go to UniProtKB: Q8DIQ1
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DIQ1
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 protein	C	461	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIF8 Go to UniProtKB: Q8DIF8
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UniProt Group	Q8DIF8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D	352	Thermosynechococcus vestitus BP-1	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8CM25 Go to UniProtKB: Q8CM25
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UniProt Group	Q8CM25
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E	83	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIP0 Go to UniProtKB: Q8DIP0
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UniProt Group	Q8DIP0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F	44	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIN9 Go to UniProtKB: Q8DIN9
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UniProt Group	Q8DIN9
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	G [auth H]	65	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJ43 Go to UniProtKB: Q8DJ43
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DJ43
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	H [auth I]	38	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJZ6 Go to UniProtKB: Q8DJZ6
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UniProt Group	Q8DJZ6
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	I [auth J]	40	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P59087 Go to UniProtKB: P59087
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59087
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	J [auth K]	37	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1K9 Go to UniProtKB: Q9F1K9
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UniProt Group	Q9F1K9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	K [auth L]	37	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIN8 Go to UniProtKB: Q8DIN8
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UniProt Group	Q8DIN8
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	L [auth M]	36	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DHA7 Go to UniProtKB: Q8DHA7
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UniProt Group	Q8DHA7
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	M [auth O]	246	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A431 Go to UniProtKB: P0A431
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UniProt Group	P0A431
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	N [auth T]	32	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIQ0 Go to UniProtKB: Q8DIQ0
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UniProt Group	Q8DIQ0
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	O [auth U]	104	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1L5 Go to UniProtKB: Q9F1L5
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UniProt Group	Q9F1L5
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	P [auth V]	137	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A386 Go to UniProtKB: P0A386
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A386
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein ycf12	Q [auth y]	46	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJI1 Go to UniProtKB: Q8DJI1
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UniProt Group	Q8DJI1
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	R [auth X]	40	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1R6 Go to UniProtKB: Q9F1R6
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UniProt Group	Q9F1R6
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	S [auth Z]	62	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DHJ2 Go to UniProtKB: Q8DHJ2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DHJ2
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Reference Sequence

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD Query on DGD Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain IC [auth D] SDF format, chain UB [auth C] SDF format, chain VB [auth C] SDF format, chain WB [auth C] MOL2 format, chain AB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain IC [auth D] MOL2 format, chain UB [auth C] MOL2 format, chain VB [auth C] MOL2 format, chain WB [auth C] mmCIF format, chain AB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain IC [auth D] mmCIF format, chain UB [auth C] mmCIF format, chain VB [auth C] mmCIF format, chain WB [auth C]	AB [auth B] CB [auth B] DA [auth A] DB [auth C] IC [auth D] AB [auth B], CB [auth B], DA [auth A], DB [auth C], IC [auth D], UB [auth C], VB [auth C], WB [auth C]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain AB [auth B] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain IC [auth D] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C] Interactions & Density Focus chain AB [auth B] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain IC [auth D] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C]
CLA Query on CLA Download:Ideal Coordinates CCD File SDF format, chain AC [auth D] SDF format, chain CC [auth D] SDF format, chain FA [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain RA [auth B] SDF format, chain RB [auth C] SDF format, chain SA [auth B] SDF format, chain SC [auth K] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain X [auth A] MOL2 format, chain AC [auth D] MOL2 format, chain CC [auth D] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain SA [auth B] MOL2 format, chain SC [auth K] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain X [auth A] mmCIF format, chain AC [auth D] mmCIF format, chain CC [auth D] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth C] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth C] mmCIF format, chain SA [auth B] mmCIF format, chain SC [auth K] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain X [auth A]	AC [auth D] CC [auth D] FA [auth A] GA [auth B] GB [auth C] AC [auth D], CC [auth D], FA [auth A], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth B], LB [auth C], MA [auth B], MB [auth C], NA [auth B], NB [auth C], OA [auth B], OB [auth C], PA [auth B], PB [auth C], QA [auth B], QB [auth C], RA [auth B], RB [auth C], SA [auth B], SC [auth K], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], X [auth A]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AC [auth D] Focus chain CC [auth D] Focus chain FA [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain SA [auth B] Focus chain SC [auth K] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain X [auth A] Interactions & Density Focus chain AC [auth D] Focus chain CC [auth D] Focus chain FA [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain SA [auth B] Focus chain SC [auth K] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain X [auth A]
PHO Query on PHO Download:Ideal Coordinates CCD File SDF format, chain BC [auth D] SDF format, chain W [auth A] MOL2 format, chain BC [auth D] MOL2 format, chain W [auth A] mmCIF format, chain BC [auth D] mmCIF format, chain W [auth A]	BC [auth D], W [auth A]	PHEOPHYTIN A C₅₅ H₇₄ N₄ O₅ CQIKWXUXPNUNDV-RCBXBCQGSA-N		Interactions Focus chain BC [auth D] Focus chain W [auth A] Interactions & Density Focus chain BC [auth D] Focus chain W [auth A]
SQD Query on SQD Download:Ideal Coordinates CCD File SDF format, chain EB [auth C] SDF format, chain HC [auth D] SDF format, chain LC [auth F] SDF format, chain UC [auth L] MOL2 format, chain EB [auth C] MOL2 format, chain HC [auth D] MOL2 format, chain LC [auth F] MOL2 format, chain UC [auth L] mmCIF format, chain EB [auth C] mmCIF format, chain HC [auth D] mmCIF format, chain LC [auth F] mmCIF format, chain UC [auth L]	EB [auth C], HC [auth D], LC [auth F], UC [auth L]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C₄₁ H₇₈ O₁₂ S RVUUQPKXGDTQPG-JUDHQOGESA-N		Interactions Focus chain EB [auth C] Focus chain HC [auth D] Focus chain LC [auth F] Focus chain UC [auth L] Interactions & Density Focus chain EB [auth C] Focus chain HC [auth D] Focus chain LC [auth F] Focus chain UC [auth L]
LMG Query on LMG Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain FC [auth D] SDF format, chain GC [auth D] SDF format, chain NC [auth I] SDF format, chain PC [auth J] SDF format, chain VC [auth M] SDF format, chain XB [auth C] SDF format, chain ZA [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain FC [auth D] MOL2 format, chain GC [auth D] MOL2 format, chain NC [auth I] MOL2 format, chain PC [auth J] MOL2 format, chain VC [auth M] MOL2 format, chain XB [auth C] MOL2 format, chain ZA [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain FC [auth D] mmCIF format, chain GC [auth D] mmCIF format, chain NC [auth I] mmCIF format, chain PC [auth J] mmCIF format, chain VC [auth M] mmCIF format, chain XB [auth C] mmCIF format, chain ZA [auth B]	CA [auth A] FC [auth D] GC [auth D] NC [auth I] PC [auth J] CA [auth A], FC [auth D], GC [auth D], NC [auth I], PC [auth J], VC [auth M], XB [auth C], ZA [auth B]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain CA [auth A] Focus chain FC [auth D] Focus chain GC [auth D] Focus chain NC [auth I] Focus chain PC [auth J] Focus chain VC [auth M] Focus chain XB [auth C] Focus chain ZA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain FC [auth D] Focus chain GC [auth D] Focus chain NC [auth I] Focus chain PC [auth J] Focus chain VC [auth M] Focus chain XB [auth C] Focus chain ZA [auth B]
PL9 Query on PL9 Download:Ideal Coordinates CCD File SDF format, chain DC [auth D] MOL2 format, chain DC [auth D] mmCIF format, chain DC [auth D]	DC [auth D]	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C₅₃ H₈₀ O₂ FKUYMLZIRPABFK-UHFFFAOYSA-N		Interactions Focus chain DC [auth D] Interactions & Density Focus chain DC [auth D]
LHG Query on LHG Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain FB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain FB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain FB [auth C]	BA [auth A], FB [auth C]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain BA [auth A] Focus chain FB [auth C] Interactions & Density Focus chain BA [auth A] Focus chain FB [auth C]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain KC [auth F] SDF format, chain ZC [auth V] MOL2 format, chain KC [auth F] MOL2 format, chain ZC [auth V] mmCIF format, chain KC [auth F] mmCIF format, chain ZC [auth V]	KC [auth F], ZC [auth V]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain KC [auth F] Focus chain ZC [auth V] Interactions & Density Focus chain KC [auth F] Focus chain ZC [auth V]
BCR Query on BCR Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AD [auth X] SDF format, chain BD [auth Z] SDF format, chain EC [auth D] SDF format, chain QC [auth J] SDF format, chain RC [auth J] SDF format, chain SB [auth C] SDF format, chain TB [auth C] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AD [auth X] MOL2 format, chain BD [auth Z] MOL2 format, chain EC [auth D] MOL2 format, chain QC [auth J] MOL2 format, chain RC [auth J] MOL2 format, chain SB [auth C] MOL2 format, chain TB [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AD [auth X] mmCIF format, chain BD [auth Z] mmCIF format, chain EC [auth D] mmCIF format, chain QC [auth J] mmCIF format, chain RC [auth J] mmCIF format, chain SB [auth C] mmCIF format, chain TB [auth C] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B]	AA [auth A] AD [auth X] BD [auth Z] EC [auth D] QC [auth J] AA [auth A], AD [auth X], BD [auth Z], EC [auth D], QC [auth J], RC [auth J], SB [auth C], TB [auth C], WA [auth B], XA [auth B], YA [auth B]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain AA [auth A] Focus chain AD [auth X] Focus chain BD [auth Z] Focus chain EC [auth D] Focus chain QC [auth J] Focus chain RC [auth J] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AD [auth X] Focus chain BD [auth Z] Focus chain EC [auth D] Focus chain QC [auth J] Focus chain RC [auth J] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain EA [auth A] SDF format, chain JC [auth D] SDF format, chain OC [auth I] SDF format, chain XC [auth O] SDF format, chain YB [auth D] SDF format, chain YC [auth T] MOL2 format, chain BB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain JC [auth D] MOL2 format, chain OC [auth I] MOL2 format, chain XC [auth O] MOL2 format, chain YB [auth D] MOL2 format, chain YC [auth T] mmCIF format, chain BB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain JC [auth D] mmCIF format, chain OC [auth I] mmCIF format, chain XC [auth O] mmCIF format, chain YB [auth D] mmCIF format, chain YC [auth T]	BB [auth B] EA [auth A] JC [auth D] OC [auth I] XC [auth O] BB [auth B], EA [auth A], JC [auth D], OC [auth I], XC [auth O], YB [auth D], YC [auth T]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain BB [auth B] Focus chain EA [auth A] Focus chain JC [auth D] Focus chain OC [auth I] Focus chain XC [auth O] Focus chain YB [auth D] Focus chain YC [auth T] Interactions & Density Focus chain BB [auth B] Focus chain EA [auth A] Focus chain JC [auth D] Focus chain OC [auth I] Focus chain XC [auth O] Focus chain YB [auth D] Focus chain YC [auth T]
OEC Query on OEC Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain Z [auth A]	Z [auth A]	OXYGEN EVOLVING SYSTEM Ca Mn₄ O₄ UFRGXNUNWYSFQE-UHFFFAOYSA-N		Interactions Focus chain Z [auth A] Interactions & Density Focus chain Z [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Y [auth A]	Y [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain ZB [auth D] MOL2 format, chain ZB [auth D] mmCIF format, chain ZB [auth D]	ZB [auth D]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain ZB [auth D] Interactions & Density Focus chain ZB [auth D]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain MC [auth F] SDF format, chain TC [auth K] SDF format, chain WC [auth O] MOL2 format, chain MC [auth F] MOL2 format, chain TC [auth K] MOL2 format, chain WC [auth O] mmCIF format, chain MC [auth F] mmCIF format, chain TC [auth K] mmCIF format, chain WC [auth O]	MC [auth F], TC [auth K], WC [auth O]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain MC [auth F] Focus chain TC [auth K] Focus chain WC [auth O] Interactions & Density Focus chain MC [auth F] Focus chain TC [auth K] Focus chain WC [auth O]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.308 (Depositor), 0.303 (DCC)
R-Value Work: 0.297 (Depositor), 0.296 (DCC)
R-Value Observed: 0.297 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.89	α = 90
b = 224.69	β = 90
c = 337.28	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
Version 2.1: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

3KZI | pdb_00003kzi

Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II

Literature

Crystal Structure of Monomeric Photosystem II from Thermosynechococcus elongatus at 3.6-A Resolution

Biological Assembly 1

Macromolecules

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