3G7F | pdb_00003g7f

Crystal structure of Blastochloris viridis heterodimer mutant reaction center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Structural and spectropotentiometric analysis of Blastochloris viridis heterodimer mutant reaction center

Ponomarenko, N.S.Li, L.Marino, A.R.Tereshko, V.Ostafin, A.Popova, J.A.Bylina, E.J.Ismagilov, R.F.Norris, J.R.

(2009) Biochim Biophys Acta 1788: 1822-1831

  • DOI: https://doi.org/10.1016/j.bbamem.2009.06.006
  • Primary Citation Related Structures: 
    3G7F

  • PubMed Abstract: 

    Heterodimer mutant reaction centers (RCs) of Blastochloris viridis were crystallized using microfluidic technology. In this mutant, a leucine residue replaced the histidine residue which had acted as a fifth ligand to the bacteriochlorophyll (BChl) of the primary electron donor dimer M site (HisM200). With the loss of the histidine-coordinated Mg, one bacteriochlorophyll of the special pair was converted into a bacteriopheophytin (BPhe), and the primary donor became a heterodimer supermolecule. The crystals had dimensions 400 x 100 x 100 microm, belonged to space group P4(3)2(1)2, and were isomorphous to the ones reported earlier for the wild type (WT) strain. The structure was solved to a 2.5 A resolution limit. Electron-density maps confirmed the replacement of the histidine residue and the absence of Mg. Structural changes in the heterodimer mutant RC relative to the WT included the absence of the water molecule that is typically positioned between the M side of the primary donor and the accessory BChl, a slight shift in the position of amino acids surrounding the site of the mutation, and the rotation of the M194 phenylalanine. The cytochrome subunit was anchored similarly as in the WT and had no detectable changes in its overall position. The highly conserved tyrosine L162, located between the primary donor and the highest potential heme C(380), revealed only a minor deviation of its hydroxyl group. Concomitantly to modification of the BChl molecule, the redox potential of the heterodimer primary donor increased relative to that of the WT organism (772 mV vs. 517 mV). The availability of this heterodimer mutant and its crystal structure provides opportunities for investigating changes in light-induced electron transfer that reflect differences in redox cascades.


  • Organizational Affiliation
    • Department of Chemistry, University of Chicago, 929 E.57th Street, GCIS, Chicago, IL 60637, USA.

Macromolecule Content 

  • Total Structure Weight: 145.58 kDa 
  • Atom Count: 10,922 
  • Modeled Residue Count: 1,178 
  • Deposited Residue Count: 1,190 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [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
Photosynthetic reaction center H subunitB [auth H]258Blastochloris viridisMutation(s): 2 
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
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center L subunitC [auth L]273Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Entity Groups
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UniProt GroupP06009
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center M subunitD [auth M]323Blastochloris viridisMutation(s): 1 
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB

Query on BCB



Download:Ideal Coordinates CCD File
IA [auth M],
Y [auth L],
Z [auth L]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB

Query on BPB



Download:Ideal Coordinates CCD File
AA [auth L],
JA [auth M],
KA [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ9

Query on MQ9



Download:Ideal Coordinates CCD File
GA [auth M]MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
E [auth C],
F [auth C],
G [auth C],
H [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
NS5

Query on NS5



Download:Ideal Coordinates CCD File
LA [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
UQ1

Query on UQ1



Download:Ideal Coordinates CCD File
BA [auth L],
HA [auth M]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
TA [auth M],
UA [auth M],
V [auth H],
W [auth H]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO

Query on HTO



Download:Ideal Coordinates CCD File
DA [auth L],
EA [auth L],
P [auth C],
Q [auth C],
X [auth H]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth L]
I [auth C]
J [auth C]
K [auth C]
L [auth C]
CA [auth L],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
M [auth C],
MA [auth M],
N [auth C],
NA [auth M],
O [auth C],
OA [auth M],
PA [auth M],
QA [auth M],
R [auth H],
RA [auth M],
S [auth H],
SA [auth M],
T [auth H],
U [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE2

Query on FE2



Download:Ideal Coordinates CCD File
FA [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D 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: 2.50 Å
  • R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.132α = 90
b = 220.132β = 90
c = 112.744γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Data collection, Structure summary