1R2C

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 101: 5982-5987

  • DOI: 10.1073/pnas.0306840101

  • 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 a ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosynthetic reaction center cytochrome C subunit precursor
C
336Blastochloris viridisGene Names: pufC (cytC)
Find proteins for P07173 (Blastochloris viridis)
Go to UniProtKB:  P07173
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein L chain
L
273Blastochloris viridisGene Names: pufL
Find proteins for P06009 (Blastochloris viridis)
Go to UniProtKB:  P06009
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein M chain
M
323Blastochloris viridisGene Names: pufM
Find proteins for P06010 (Blastochloris viridis)
Go to UniProtKB:  P06010
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein H chain
H
258Blastochloris viridisGene Names: puhA
Find proteins for P06008 (Blastochloris viridis)
Go to UniProtKB:  P06008
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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H, M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LDA
Query on LDA

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H, L, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MQ7
Query on MQ7

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M
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
FE2
Query on FE2

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M
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
BPB
Query on BPB

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L, M
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
UQ2
Query on UQ2

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L
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
BCB
Query on BCB

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L, M
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
NS5
Query on NS5

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M
15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
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 
  • R-Value Work: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 223.500α = 90.00
b = 223.500β = 90.00
c = 112.500γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance