2X5V

80 microsecond laue diffraction snapshot from crystals of a photosynthetic reaction centre 3 millisecond following photoactivation.

PDB DOI: https://doi.org/10.2210/pdb2X5V/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Blastochloris viridis
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2010-02-10 Released: 2010-05-12
Deposition Author(s): Wohri, A.B., Katona, G., Johansson, L.C., Fritz, E., Malmerberg, E., Andersson, M., Vincent, J., Eklund, M., Cammarata, M., Wulff, M., Davidsson, J., Groenhof, G., Neutze, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.319
R-Value Work: 0.277
R-Value Observed: 0.279

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Light-Induced Structural Changes in a Photosynthetic Reaction Center Caught by Laue Diffraction.

Wohri, A.B., Katona, G., Johansson, L.C., Fritz, E., Malmerberg, E., Andersson, M., Vincent, J., Eklund, M., Cammarata, M., Wulff, M., Davidsson, J., Groenhof, G., Neutze, R.

(2010) Science 328: 630

PubMed: 20431017 Search on PubMed
DOI: https://doi.org/10.1126/science.1186159
Primary Citation of Related Structures:
2X5U, 2X5V

PubMed Abstract:
Photosynthetic reaction centers convert the energy content of light into a transmembrane potential difference and so provide the major pathway for energy input into the biosphere. We applied time-resolved Laue diffraction to study light-induced conformational changes in the photosynthetic reaction center complex of Blastochloris viridis. The side chain of TyrL162, which lies adjacent to the special pair of bacteriochlorophyll molecules that are photooxidized in the primary light conversion event of photosynthesis, was observed to move 1.3 angstroms closer to the special pair after photoactivation. Free energy calculations suggest that this movement results from the deprotonation of this conserved tyrosine residue and provides a mechanism for stabilizing the primary charge separation reactions of photosynthesis.

Organizational Affiliation

Department of Chemical and Biological Engineering, Chalmers University of Technology, Box 462, SE-40530 Göteborg, Sweden.

Macromolecule Content

Total Structure Weight: 141.26 kDa
Atom Count: 9,871
Modelled Residue Count: 1,171
Deposited Residue Count: 1,192
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT	A [auth C]	336	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07173
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 H CHAIN	B [auth H]	258	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008 Go to UniProtKB: P06008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06008
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN L CHAIN	C [auth L]	274	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06009
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN M CHAIN	D [auth M]	324	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB Query on BCB Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain M SDF format, chain L [auth M] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain M MOL2 format, chain L [auth M]	I [auth L], J [auth L], L [auth M], M	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain I [auth L] Focus chain J [auth L] Focus chain L [auth M] Focus chain M Interactions & Density Focus chain I [auth L] Focus chain J [auth L] Focus chain L [auth M] Focus chain M
BPB Query on BPB Download Ideal Coordinates CCD File SDF format, chain N [auth M] SDF format, chain K [auth L] MOL2 format, chain N [auth M] MOL2 format, chain K [auth L]	K [auth L], N [auth M]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain K [auth L] Focus chain N [auth M] Interactions & Density Focus chain K [auth L] Focus chain N [auth M]
MQ7 Query on MQ7 Download Ideal Coordinates CCD File SDF format, chain P [auth M] MOL2 format, chain P [auth M]	P [auth M]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain P [auth M] Interactions & Density Focus chain P [auth M]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] MOL2 format, chain G [auth C] MOL2 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]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain O [auth M] MOL2 format, chain O [auth M]	O [auth M]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain O [auth M] Interactions & Density Focus chain O [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: 3.00 Å
R-Value Free: 0.319
R-Value Work: 0.277
R-Value Observed: 0.279
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.693	α = 90
b = 143.47	β = 90
c = 177.998	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Precognition	data reduction
Epinorm	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2012-02-01
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-01-25
Changes: Data collection
Version 1.3: 2019-05-22
Changes: Advisory, Data collection, Derived calculations, Experimental preparation
Version 2.0: 2019-09-25
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description