1EYS

CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.

Nogi, T.Fathir, I.Kobayashi, M.Nozawa, T.Miki, K.

(2000) Proc Natl Acad Sci U S A 97: 13561-13566

  • DOI: 10.1073/pnas.240224997
  • Primary Citation of Related Structures:  
    1EYT, 1EYS

  • PubMed Abstract: 
  • The reaction center (RC) of photosynthetic bacteria is a membrane protein complex that promotes a light-induced charge separation during the primary process of photosynthesis. In the photosynthetic electron transfer chain, the soluble electron carrier proteins transport electrons to the RC and reduce the photo-oxidized special-pair of bacteriochlorophyll ...

    The reaction center (RC) of photosynthetic bacteria is a membrane protein complex that promotes a light-induced charge separation during the primary process of photosynthesis. In the photosynthetic electron transfer chain, the soluble electron carrier proteins transport electrons to the RC and reduce the photo-oxidized special-pair of bacteriochlorophyll. The high-potential iron-sulfur protein (HiPIP) is known to serve as an electron donor to the RC in some species, where the c-type cytochrome subunit, the peripheral subunit of the RC, directly accepts electrons from the HiPIP. Here we report the crystal structures of the RC and the HiPIP from Thermochromatium (Tch.) tepidum, at 2.2-A and 1.5-A resolution, respectively. Tch. tepidum can grow at the highest temperature of all known purple bacteria, and the Tch. tepidum RC shows some degree of stability to high temperature. Comparison with the RCs of mesophiles, such as Blastochloris viridis, has shown that the Tch. tepidum RC possesses more Arg residues at the membrane surface, which might contribute to the stability of this membrane protein. The RC and the HiPIP both possess hydrophobic patches on their respective surfaces, and the HiPIP is expected to interact with the cytochrome subunit by hydrophobic interactions near the heme-1, the most distal heme to the special-pair.


    Related Citations: 
    • Preliminary X-ray Crystallographic Studies of Photosynthetic Reaction Center from a Thermophilic Sulfur Bacterium, Chromatium tepidum
      Katayama, N., Kobayashi, M., Motojima, F., Inaka, K., Nozawa, T., Miki, K.
      (1994) FEBS Lett 348: 158

    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERA [auth C]382Thermochromatium tepidumMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERB [auth L]280Thermochromatium tepidumMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERC [auth M]324Thermochromatium tepidumMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERD [auth H]259Thermochromatium tepidumMutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for Q93RD8 (Thermochromatium tepidum)
Explore Q93RD8 
Go to UniProtKB:  Q93RD8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

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

Download Ideal Coordinates CCD File 
N [auth L], V [auth M]BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
MQ8
Query on MQ8

Download Ideal Coordinates CCD File 
W [auth M]MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
 Ligand Interaction
PEF
Query on PEF

Download Ideal Coordinates CCD File 
Y [auth H]DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth C], F [auth C], G [auth C], H [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CRT
Query on CRT

Download Ideal Coordinates CCD File 
X [auth M]SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
 Ligand Interaction
BGL
Query on BGL

Download Ideal Coordinates CCD File 
I [auth L], J [auth L], K [auth L], P [auth M], Q [auth M], R [auth M]2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
 Ligand Interaction
LDA
Query on LDA

Download Ideal Coordinates CCD File 
O [auth L]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
S [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.299α = 90
b = 196.596β = 90
c = 84.163γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary