3I4D

Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of the carotenoid bound to the reaction centre from Rhodobacter sphaeroides 2.4.1 revealed by time-resolved X-ray crystallography

Fujii, R.Adachi, S.Roszak, A.W.Gardiner, A.T.Cogdell, R.J.Isaacs, N.W.Koshihara, S.Hashimoto, H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]281Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M]307Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
BB [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
BCL
Query on BCL

Download Ideal Coordinates CCD File 
D [auth L],
E [auth L],
MA [auth M],
NA [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH
Query on BPH

Download Ideal Coordinates CCD File 
F [auth L],
OA [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10
Query on U10

Download Ideal Coordinates CCD File 
G [auth L],
QA [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
SPO
Query on SPO

Download Ideal Coordinates CCD File 
RA [auth M]SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
 Ligand Interaction
UQ1
Query on UQ1

Download Ideal Coordinates CCD File 
H [auth L]UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
LDA
Query on LDA

Download Ideal Coordinates CCD File 
BA [auth L],
CA [auth L],
CB [auth M],
DA [auth L],
DB [auth M],
BA [auth L],
CA [auth L],
CB [auth M],
DA [auth L],
DB [auth M],
EA [auth L],
EB [auth M],
FA [auth L],
FB [auth M],
GA [auth L],
GB [auth M],
HA [auth L],
HB [auth M],
IA [auth L],
JA [auth L],
KA [auth L],
LA [auth L],
UB [auth H],
VB [auth H],
WB [auth H],
XB [auth H]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

Download Ideal Coordinates CCD File 
AA [auth L],
TB [auth H]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
HT3
Query on HT3

Download Ideal Coordinates CCD File 
Z [auth L](2R,3S)-heptane-1,2,3-triol
C7 H16 O3
HXYCHJFUBNTKQR-NKWVEPMBSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth L],
J [auth L],
JB [auth H],
K [auth L],
L,
I [auth L],
J [auth L],
JB [auth H],
K [auth L],
L,
UA [auth M],
VA [auth M]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth M],
KB [auth H],
LB [auth H],
MB [auth H],
N [auth L],
AB [auth M],
KB [auth H],
LB [auth H],
MB [auth H],
N [auth L],
NB [auth H],
O [auth L],
OB [auth H],
P [auth L],
PB [auth H],
Q [auth L],
QB [auth H],
R [auth L],
RB [auth H],
S [auth L],
SB [auth H],
T [auth L],
U [auth L],
V [auth L],
W [auth L],
WA [auth M],
X [auth L],
XA [auth M],
Y [auth L],
YA [auth M],
ZA [auth M]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download Ideal Coordinates CCD File 
M [auth L]1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
PA [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
IB [auth H],
SA [auth M]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
TA [auth M]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.8α = 90
b = 138.8β = 90
c = 184.569γ = 120
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance