2BNP

Lipidic cubic phase grown reaction centre from Rhodobacter sphaeroides, ground state

PDB DOI: https://doi.org/10.2210/pdb2BNP/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2005-03-31 Released: 2005-05-27
Deposition Author(s): Katona, G., Snijder, A., Gourdon, P., Andreasson, U., Hansson, O., Andreasson, L.E., Neutze, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.249
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Conformational Regulation of Charge Recombination Reactions in a Photosynthetic Bacterial Reaction Centre

Katona, G., Snijder, A., Gourdon, P., Andreasson, U., Hansson, O., Andreasson, L.E., Neutze, R.

(2005) Nat Struct Mol Biol 12: 630

PubMed: 15937492 Search on PubMed
DOI: https://doi.org/10.1038/nsmb948
Primary Citation of Related Structures:
2BNP, 2BNS

PubMed Abstract:
In bright light the photosynthetic reaction center (RC) of Rhodobacter sphaeroides stabilizes the P(+)(870).Q(-)(A) charge-separated state and thereby minimizes the potentially harmful effects of light saturation. Using X-ray diffraction we report a conformational change that occurs within the cytoplasmic domain of this RC in response to prolonged illumination with bright light. Our observations suggest a novel structural mechanism for the regulation of electron transfer reactions in photosynthesis.

Organizational Affiliation

Chalmers University of Technology, Department of Chemistry and Bioscience, PO Box 462, SE-405 30 Göteborg, Sweden.

Macromolecule Content

Total Structure Weight: 100.62 kDa
Atom Count: 6,935
Modelled Residue Count: 820
Deposited Residue Count: 848
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	A	281	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8 Go to UniProtKB: P0C0Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	B	307	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9 Go to UniProtKB: P0C0Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	C	260	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7 Go to UniProtKB: P0C0Y7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
MST Query on MST Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE C₁₀ H₁₉ N₅ S IROINLKCQGIITA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	N [auth B], O [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.249
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.142	α = 90
b = 100.142	β = 90
c = 238.002	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-05-27
Type: Initial release
Version 1.1: 2013-03-20
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2019-09-25
Changes: Advisory, Data collection, Database references, Experimental preparation, Other, Source and taxonomy, Structure summary
Version 1.3: 2023-12-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description