1R2C | pdb_00001r2c

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 
    0.228 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center.

Baxter, R.H.Ponomarenko, N.Srajer, V.Pahl, R.Moffat, K.Norris, J.R.

(2004) Proc Natl Acad Sci U S A 101: 5982-5987

  • DOI: https://doi.org/10.1073/pnas.0306840101
  • Primary Citation Related Structures: 
    1R2C

  • PubMed Abstract: 

    Light-induced structural changes in the bacterial reaction center were studied by a time-resolved crystallographic experiment. Crystals of protein from Blastochloris viridis (formerly Rhodopseudomonas viridis) were reconstituted with ubiquinone and analyzed by monochromatic and Laue diffraction, in the dark and 3 ms after illuminating the crystal with a pulsed laser (630 nm, 3 mJ/pulse, 7 ns duration). Refinement of monochromatic data shows that ubiquinone binds only in the "proximal" Q(B) binding site. No significant structural difference was observed between the light and dark datasets; in particular, no quinone motion was detected. This result may be reconciled with previous studies by postulating equilibration of the "distal" and "proximal" binding sites upon extended dark adaption, and in which movement of ubiquinone is not the conformational gate for the first electron transfer between Q(A) and Q(B).


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

Macromolecule Content 

  • Total Structure Weight: 143.61 kDa 
  • Atom Count: 10,140 
  • Modeled Residue Count: 1,186 
  • Deposited Residue Count: 1,190 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome C subunit precursorA [auth C]336Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07173 (Blastochloris viridis)
Explore P07173 
Go to UniProtKB:  P07173
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07173
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]273Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06009
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]323Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Entity Groups
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UniProt GroupP06010
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein H chainD [auth H]258Blastochloris viridisMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P06008 (Blastochloris viridis)
Explore P06008 
Go to UniProtKB:  P06008
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06008
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB

Query on BCB



Download:Ideal Coordinates CCD File
I [auth L],
J [auth L],
R [auth M],
S [auth M]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB

Query on BPB



Download:Ideal Coordinates CCD File
K [auth L],
T [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ7

Query on MQ7



Download:Ideal Coordinates CCD File
U [auth M]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
E [auth C],
F [auth C],
G [auth C],
H [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NS5

Query on NS5



Download:Ideal Coordinates CCD File
V [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
UQ2

Query on UQ2



Download:Ideal Coordinates CCD File
L
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
BA [auth H]
M [auth L]
W [auth M]
X [auth M]
Y [auth M]
BA [auth H],
M [auth L],
W [auth M],
X [auth M],
Y [auth M],
Z [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth H],
O [auth M],
P [auth M],
Q [auth M]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE2

Query on FE2



Download:Ideal Coordinates CCD File
N [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
D [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free:  0.228 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.5α = 90
b = 223.5β = 90
c = 112.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary