3WMM

Crystal structure of the LH1-RC complex from Thermochromatium tepidum in C2 form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.337
  • R-Value Work: 0.314

Literature

Macromolecules
Sequence Display for 3WMM

Classification: PHOTOSYNTHESIS

Total Structure Weight: 392577.13

Macromolecule Entities
Molecule Chains Length Organism Details
Photosynthetic reaction center C subunit C 404 Thermochromatium tepidum Gene Name(s): pufC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosynthetic reaction center L subunit L 281 Thermochromatium tepidum Gene Name(s): pufL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosynthetic reaction center M subunit M 325 Thermochromatium tepidum Gene Name(s): pufM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosynthetic reaction center H subunit H 259 Thermochromatium tepidum Gene Name(s): puhA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LH1 alpha polypeptide 1, 3, 5..., 7, 9, A, D, F, I, K, O, Q, S, U, W, Y1, 3, 5, 7, 9, A, D, F, I, K, O, Q, S, U, W, Y 61 Thermochromatium tepidum Gene Name(s): pufA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LH1 beta polypeptide 0, 2, 4..., 6, 8, B, E, G, J, N, P, R, T, V, X, Z0, 2, 4, 6, 8, B, E, G, J, N, P, R, T, V, X, Z 47 Thermochromatium tepidum Gene Name(s): pufB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Light-Harvesting+Reaction Center Complexes

Protein Name: LH1-RC complex, P21 crystal form


Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BCL
Query on BCL

0, 1, 2, 3, 4, 5, 6, 7, 9, A, B, D, E, F, G, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BPH
Query on BPH

L, M BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGW
Query on PGW

H, M (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}- 1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec- 9-enoate
1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho- (1-glycerol)]; PHOSPHATIDYLGLYCEROL (Synonym)
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UQ8
Query on UQ8

L Ubiquinone-8
2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)- 3,7,11,15,19,23,27,31-octamethyldotriaconta- 2,6,10,14,18,22,26,30-octaen-1-yl]cyclohexa- 2,5-diene-1,4-dione (Synonym)
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MQ8
Query on MQ8

M MENAQUINONE 8
7, (Synonym)
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEF
Query on PEF

H DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]- SN-GLYCEROL (Synonym)
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CRT
Query on CRT

2, 3, 4, 8, A, B, G, J, M, N, P, R, T, V, W, X SPIRILLOXANTHIN
RHODOVIOLASCIN (Synonym)
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

H, L, M PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

M FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

1, 3, 5, 7, 9, A, C, D, F, I, K, O, Q, S, U, W, Y CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.337
  • R-Value Work: 0.314
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 227.34 α = 90.00
b = 148.24 β = 117.59
c = 161.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-11-22
  • Released Date: 2014-04-09
  • Deposition author(s): Niwa, S., Takeda, K., Wang-Otomo, Z.-Y., Miki, K.

Revision History

  • Version 1_0: 2014-04-09

    Type: Initial release

  • Version 1_1: 2014-04-16

    Type: Database references

  • Version 1_2: 2017-06-07

    Type: Other