1VRN | pdb_00001vrn

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)

PDB DOI: https://doi.org/10.2210/pdb1VRN/pdb
Entry: 1VRN supersedes: 1TXW

Classification: PHOTOSYNTHESIS
Organism(s): Blastochloris viridis
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2005-02-23 Released: 2005-03-22
Deposition Author(s): Baxter, R.H.G., Seagle, B.-L., Norris, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.212 (Depositor), 0.208 (DCC)
R-Value Work:
0.191 (Depositor), 0.187 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark.

Baxter, R.H., Seagle, B.L., Ponomarenko, N., Norris, J.R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 605-612

PubMed: 15858271 Search on PubMed
DOI: https://doi.org/10.1107/S0907444905005809
Primary Citation Related Structures:
1VRN

PubMed Abstract:
The structure of the Blastochloris viridis photosynthetic reaction center has been determined at 100 K by flash-freezing crystals. A data set to 2.2 A resolution provides a well determined model of the wild-type protein. Of particular interest are the position, occupancy and heterogeneity of the Q(B)-binding site. Data were also collected from a crystal frozen immediately after illumination. The data support predominant binding of Q(B) in the proximal position in both the neutral and charge-separated states.

Organizational Affiliation

Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA.

Macromolecule Content

Total Structure Weight: 144.04 kDa
Atom Count: 10,747
Modeled Residue Count: 1,186
Deposited Residue Count: 1,186
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	332	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173 Go to UniProtKB: P07173
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07173
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	B [auth H]	258	Blastochloris viridis	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008 Go to UniProtKB: P06008
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06008
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	C [auth L]	273	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009 Go to UniProtKB: P06009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06009
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	D [auth M]	323	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010 Go to UniProtKB: P06010
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB Query on BCB Download:Ideal Coordinates CCD File SDF format, chain Z [auth M] SDF format, chain Y [auth M] SDF format, chain O [auth L] SDF format, chain N [auth L] MOL2 format, chain Z [auth M] MOL2 format, chain Y [auth M] MOL2 format, chain O [auth L] MOL2 format, chain N [auth L] mmCIF format, chain Z [auth M] mmCIF format, chain Y [auth M] mmCIF format, chain O [auth L] mmCIF format, chain N [auth L]	N [auth L], O [auth L], Y [auth M], Z [auth M]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain N [auth L] Focus chain O [auth L] Focus chain Y [auth M] Focus chain Z [auth M] Interactions & Density Focus chain N [auth L] Focus chain O [auth L] Focus chain Y [auth M] Focus chain Z [auth M]
BPB Query on BPB Download:Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain P [auth L] MOL2 format, chain AA [auth M] MOL2 format, chain P [auth L] mmCIF format, chain AA [auth M] mmCIF format, chain P [auth L]	AA [auth M], P [auth L]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain AA [auth M] Focus chain P [auth L] Interactions & Density Focus chain AA [auth M] Focus chain P [auth L]
MQ9 Query on MQ9 Download:Ideal Coordinates CCD File SDF format, chain BA [auth M] MOL2 format, chain BA [auth M] mmCIF format, chain BA [auth M]	BA [auth M]	MENAQUINONE-9 C₅₆ H₈₀ O₂ WCRXHNIUHQUASO-ABFXHILCSA-N		Interactions Focus chain BA [auth M] Interactions & Density Focus chain BA [auth M]
UQ7 Query on UQ7 Download:Ideal Coordinates CCD File SDF format, chain Q [auth L] MOL2 format, chain Q [auth L] mmCIF format, chain Q [auth L]	Q [auth L]	UBIQUINONE-7 C₄₄ H₆₆ O₄ DBESHHFMIFSNRV-RJYQSXAYSA-N		Interactions Focus chain Q [auth L] Interactions & Density Focus chain Q [auth L]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C]	E [auth C], F [auth C], G [auth C], H [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C]
NS5 Query on NS5 Download:Ideal Coordinates CCD File SDF format, chain CA [auth M] MOL2 format, chain CA [auth M] mmCIF format, chain CA [auth M]	CA [auth M]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain CA [auth M] Interactions & Density Focus chain CA [auth M]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain DA [auth M] SDF format, chain EA [auth M] SDF format, chain S [auth L] SDF format, chain R [auth L] SDF format, chain M [auth H] SDF format, chain L [auth H] MOL2 format, chain DA [auth M] MOL2 format, chain EA [auth M] MOL2 format, chain S [auth L] MOL2 format, chain R [auth L] MOL2 format, chain M [auth H] MOL2 format, chain L [auth H] mmCIF format, chain DA [auth M] mmCIF format, chain EA [auth M] mmCIF format, chain S [auth L] mmCIF format, chain R [auth L] mmCIF format, chain M [auth H] mmCIF format, chain L [auth H]	DA [auth M] EA [auth M] L [auth H] M [auth H] R [auth L] DA [auth M], EA [auth M], L [auth H], M [auth H], R [auth L], S [auth L]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain DA [auth M] Focus chain EA [auth M] Focus chain L [auth H] Focus chain M [auth H] Focus chain R [auth L] Focus chain S [auth L] Interactions & Density Focus chain DA [auth M] Focus chain EA [auth M] Focus chain L [auth H] Focus chain M [auth H] Focus chain R [auth L] Focus chain S [auth L]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain V [auth M] SDF format, chain X [auth M] SDF format, chain W [auth M] SDF format, chain U [auth M] SDF format, chain K [auth H] SDF format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain V [auth M] MOL2 format, chain X [auth M] MOL2 format, chain W [auth M] MOL2 format, chain U [auth M] MOL2 format, chain K [auth H] MOL2 format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain V [auth M] mmCIF format, chain X [auth M] mmCIF format, chain W [auth M] mmCIF format, chain U [auth M] mmCIF format, chain K [auth H] mmCIF format, chain I [auth H]	I [auth H] J [auth H] K [auth H] U [auth M] V [auth M] I [auth H], J [auth H], K [auth H], U [auth M], V [auth M], W [auth M], X [auth M]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain U [auth M] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M] Interactions & Density Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain U [auth M] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain T [auth M] MOL2 format, chain T [auth M] mmCIF format, chain T [auth M]	T [auth M]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain T [auth M] Interactions & Density Focus chain T [auth M]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	B [auth H]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.212 (Depositor), 0.208 (DCC)
R-Value Work: 0.191 (Depositor), 0.187 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 219.4	α = 90
b = 219.4	β = 90
c = 112.6	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-03-22

Deposition Author(s):

Baxter, R.H.G.

Seagle, B.-L.

Norris, J.R.

This entry supersedes: 1TXW

Revision History (Full details and data files)

Version 1.0: 2005-03-22
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2011-11-16
Changes: Atomic model
Version 2.0: 2021-03-03
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-23
Changes: Advisory, Data collection, Database references, Refinement description
Version 2.2: 2024-11-20
Changes: Data collection, Structure summary

1VRN | pdb_00001vrn

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)

Literature

Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)