1VRN

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark.

Baxter, R.H.Seagle, B.L.Ponomarenko, N.Norris, J.R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 605-612

  • DOI: 10.1107/S0907444905005809
  • Primary Citation of Related Structures:  
    1VRN

  • PubMed Abstract: 
  • The structure of the Blastochloris viridis photosynthetic reaction center has been determined at 100 K by flash-freezing crystals. A data set to 2.2 A resolution provides a well determined model of the wild-type protein. Of particular interest are the position, occupancy and heterogeneity of the Q(B)-binding site ...

    The structure of the Blastochloris viridis photosynthetic reaction center has been determined at 100 K by flash-freezing crystals. A data set to 2.2 A resolution provides a well determined model of the wild-type protein. Of particular interest are the position, occupancy and heterogeneity of the Q(B)-binding site. Data were also collected from a crystal frozen immediately after illumination. The data support predominant binding of Q(B) in the proximal position in both the neutral and charge-separated states.


    Related Citations: 
    • Specific radiation damage illustrates light-induced structural changes in the photosynthetic reaction center
      Baxter, R.H.G., Seagle, B.-L., Ponomarenko, N., Norris, J.R.
      (2004) J Am Chem Soc 126: 16728

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]332Blastochloris viridisMutation(s): 0 
Gene Names: pufCcytCBVIRIDIS_00500
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein H chainB [auth H]258Blastochloris viridisMutation(s): 1 
Gene Names: puhA
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein L chainC [auth L]273Blastochloris viridisMutation(s): 0 
Gene Names: pufL
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein M chainD [auth M]323Blastochloris viridisMutation(s): 0 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06010
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCB
Query on BCB

Download Ideal Coordinates CCD File 
N [auth L],
O [auth L],
Y [auth M],
Z [auth M]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
BPB
Query on BPB

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AA [auth M],
P [auth L]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
MQ9
Query on MQ9

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BA [auth M]MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
 Ligand Interaction
UQ7
Query on UQ7

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Q [auth L]UBIQUINONE-7
C44 H66 O4
DBESHHFMIFSNRV-RJYQSXAYSA-N
 Ligand Interaction
HEC
Query on HEC

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E [auth C],
F [auth C],
G [auth C],
H [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
NS5
Query on NS5

Download Ideal Coordinates CCD File 
CA [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
 Ligand Interaction
LDA
Query on LDA

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DA [auth M],
EA [auth M],
L [auth H],
M [auth H],
R [auth L],
DA [auth M],
EA [auth M],
L [auth H],
M [auth H],
R [auth L],
S [auth L]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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I [auth H],
J [auth H],
K [auth H],
U [auth M],
V [auth M],
I [auth H],
J [auth H],
K [auth H],
U [auth M],
V [auth M],
W [auth M],
X [auth M]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

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T [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
B [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.4α = 90
b = 219.4β = 90
c = 112.6γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
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: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary