Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis.

Deisenhofer, J; Epp, O; Sinning, I; Michel, H.

Macromolecule Content

Unique protein chains: 4

1PRC

CRYSTALLOGRAPHIC REFINEMENT AT 2.3 ANGSTROMS RESOLUTION AND REFINED MODEL OF THE PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS

DOI: 10.2210/pdb1prc/pdb

Classification: PHOTOSYNTHETIC REACTION CENTER
Deposited: 1988-02-04 Released: 1989-01-09
Deposition author(s): Deisenhofer, J., Epp, O., Miki, K., Huber, R., Michel, H.
Organism: Blastochloris viridis

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.3 Å
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: PHOTOSYNTHETIC REACTION CENTER

Total Structure Weight: 142915.13

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
PHOTOSYNTHETIC REACTION CENTER	C	336	Blastochloris viridis	Gene Name(s): pufC cytC BVIRIDIS_00500
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P07173 UniProt Full Protein Feature View for P07173 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P07173/1PRC
PHOTOSYNTHETIC REACTION CENTER	L	273	Blastochloris viridis	Gene Name(s): pufL
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P06009 UniProt Full Protein Feature View for P06009 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P06009/1PRC
PHOTOSYNTHETIC REACTION CENTER	M	323	Blastochloris viridis	Gene Name(s): pufM
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P06010 UniProt Full Protein Feature View for P06010 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P06010/1PRC
PHOTOSYNTHETIC REACTION CENTER	H	258	Blastochloris viridis	Gene Name(s): puhA
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P06008 UniProt Full Protein Feature View for P06008 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P06008/1PRC

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Photosynthetic Reaction Centers

Protein Name: Photosynthetic Reaction Center

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
BCB Query on BCB Download SDF File Download CCD File	L, M	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-LQPBATPMDK	Poseview Image of BCB in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
BPB Query on BPB Download SDF File Download CCD File	L, M	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N	Poseview Image of BPB in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
MQ7 Query on MQ7 Download SDF File Download CCD File	M	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N	Poseview Image of MQ7 in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
HEM Query on HEM Download SDF File Download CCD File	C	PROTOPORPHYRIN IX CONTAINING FE HEME (Synonym) C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L	Poseview Image of HEM in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
NS1 Query on NS1 Download SDF File Download CCD File	M	15-trans-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-HFHFAFRXSA-N	Poseview Image of NS1 in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
UQ1 Query on UQ1 Download SDF File Download CCD File	L	UBIQUINONE-1 C₁₄ H₁₈ O₄ SOECUQMRSRVZQQ-UHFFFAOYSA-N	Poseview Image of UQ1 in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
LDA Query on LDA Download SDF File Download CCD File	H, M	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N	Poseview Image of LDA in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
SO4 Query on SO4 Download SDF File Download CCD File	H, M	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L	Poseview Image of SO4 in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
FE Query on FE Download SDF File Download CCD File	M	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N	Poseview Image of FE in 1PRC Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.3 Å
R-Value Observed: 0.193
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 223.50	α = 90.00
b = 223.50	β = 90.00
c = 113.60	γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 1988-02-04
Released Date: 1989-01-09
Deposition author(s): Deisenhofer, J., Epp, O., Miki, K., Huber, R., Michel, H.

Revision History

Version 1_0: 1989-01-09
Type: Initial release
Version 1_1: 2008-03-21
Type: Version format compliance
Version 1_2: 2011-07-13
Type: Non-polymer description, Version format compliance
Version 1_3: 2014-08-13
Type: Other

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