3T6D

Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC 19567) substrain-08


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory.

Roszak, A.W.Moulisova, V.Reksodipuro, A.D.Gardiner, A.T.Fujii, R.Hashimoto, H.Isaacs, N.W.Cogdell, R.J.

(2012) Biochem J 442: 27-37

  • DOI: https://doi.org/10.1042/BJ20111540
  • Primary Citation of Related Structures:  
    3T6D, 3T6E

  • PubMed Abstract: 

    Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.


  • Organizational Affiliation

    WestCHEM, School of Chemistry, College of Science and Engineering, University of Glasgow, Glasgow Biomedical Research Centre, 120 University Place, Glasgow G12 8TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]356Blastochloris 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): 0 
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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06009
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center M-subunitD [auth M]323Blastochloris viridisMutation(s): 0 
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 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB
Query on BCB

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NC [auth L],
OC [auth L],
SD [auth M],
TD [auth M]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB
Query on BPB

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PC [auth L],
UD [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
UQ9
Query on UQ9

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QC [auth L],
RC [auth L]
Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
MQ9
Query on MQ9

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RD [auth M]MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
DGA
Query on DGA

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K [auth C]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
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
NS5
Query on NS5

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VD [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
LDA
Query on LDA

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AD [auth L]
AE [auth M]
BB [auth H]
BE [auth M]
CB [auth H]
AD [auth L],
AE [auth M],
BB [auth H],
BE [auth M],
CB [auth H],
CE [auth M],
DB [auth H],
DE [auth M],
EB [auth H],
FB [auth H],
I [auth C],
J [auth C],
SC [auth L],
TC [auth L],
UC [auth L],
VC [auth L],
WC [auth L],
WD [auth M],
XC [auth L],
XD [auth M],
YC [auth L],
YD [auth M],
ZC [auth L],
ZD [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTH
Query on HTH

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ME [auth M](2S,3R)-heptane-1,2,3-triol
C7 H16 O3
HXYCHJFUBNTKQR-RQJHMYQMSA-N
HTO
Query on HTO

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DA [auth C]
DD [auth L]
EA [auth C]
ED [auth L]
FA [auth C]
DA [auth C],
DD [auth L],
EA [auth C],
ED [auth L],
FA [auth C],
FD [auth L],
GA [auth C],
GD [auth L],
HD [auth L],
NE [auth M],
TB [auth H],
UB [auth H],
VB [auth H]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
SO4
Query on SO4

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AA [auth C]
BA [auth C]
BD [auth L]
CA [auth C]
CD [auth L]
AA [auth C],
BA [auth C],
BD [auth L],
CA [auth C],
CD [auth L],
EE [auth M],
FE [auth M],
GB [auth H],
GE [auth M],
HB [auth H],
HE [auth M],
IB [auth H],
IE [auth M],
JB [auth H],
JE [auth M],
KB [auth H],
KE [auth M],
L [auth C],
LB [auth H],
LE [auth M],
M [auth C],
MB [auth H],
N [auth C],
NB [auth H],
O [auth C],
OB [auth H],
P [auth C],
PB [auth H],
Q [auth C],
QB [auth H],
R [auth C],
RB [auth H],
S [auth C],
SB [auth H],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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AB [auth C]
AC [auth H]
BC [auth H]
CC [auth H]
DC [auth H]
AB [auth C],
AC [auth H],
BC [auth H],
CC [auth H],
DC [auth H],
EC [auth H],
FC [auth H],
GC [auth H],
HA [auth C],
HC [auth H],
IA [auth C],
IC [auth H],
ID [auth L],
JA [auth C],
JC [auth H],
JD [auth L],
KA [auth C],
KC [auth H],
KD [auth L],
LA [auth C],
LC [auth H],
LD [auth L],
MA [auth C],
MC [auth H],
MD [auth L],
NA [auth C],
ND [auth L],
OA [auth C],
OD [auth L],
OE [auth M],
PA [auth C],
PD [auth L],
PE [auth M],
QA [auth C],
QE [auth M],
RA [auth C],
RE [auth M],
SA [auth C],
SE [auth M],
TA [auth C],
TE [auth M],
UA [auth C],
UE [auth M],
VA [auth C],
VE [auth M],
WA [auth C],
WB [auth H],
WE [auth M],
XA [auth C],
XB [auth H],
YA [auth C],
YB [auth H],
ZA [auth C],
ZB [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
QD [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: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.44α = 90
b = 220.44β = 90
c = 113.1γ = 90
Software Package:
Software NamePurpose
DNAdata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Advisory, Data collection, Database references, Refinement description