1DXR

Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant (terbutryn complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 1DXR

Classification: PHOTOSYNTHESIS

Total Structure Weight: 143688.94

Macromolecule Entities
Molecule Chains Length Organism Details
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT C 336 Blastochloris viridis Gene Name(s): pufC cytC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYNTHETIC REACTION CENTER H SUBUNIT H 258 Blastochloris viridis Gene Name(s): puhA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYNTHETIC REACTION CENTER L SUBUNIT L 273 Blastochloris viridis Mutation: H168F
Gene Name(s): pufL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYNTHETIC REACTION CENTER M SUBUNIT M 323 Blastochloris viridis Gene Name(s): pufM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Photosynthetic Reaction Centers

Protein Name: Photosynthetic Reaction Center


Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BCB
Query on BCB

L, M BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BPB
Query on BPB

L, M BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MQ9
Query on MQ9

L MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEC
Query on HEC

C HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NS5
Query on NS5

M 15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MST
Query on MST

L 2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO- S-TRIAZINE
C10 H19 N5 S
IROINLKCQGIITA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LDA
Query on LDA

H, L, M LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

H, M SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

L FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FME
Query on FME
H L-PEPTIDE LINKING C6 H11 N O3 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.194
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 223.50 α = 90.00
b = 223.50 β = 90.00
c = 113.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-01-15
  • Released Date: 2001-01-12
  • Deposition author(s): Lancaster, C.R.D., Bibikova, M., Sabatino, P., Oesterhelt, D., Michel, H.

Revision History

  • 2011-07-27
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • 2012-02-08
    Type: Other
  • 2014-09-03
    Type: Database references, Structure summary