3C9L

Structure of ground-state bovine rhodospin in a hexagonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.646 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 1GZM - determined by Li, J.  

Literature

Alternative models for two crystal structures of bovine rhodopsin.

Stenkamp, R.E.

(2008) Acta Crystallogr.,Sect.D 64: 902-904

  • DOI: 10.1107/S0907444908017162
  • Primary Citation of Related Structures:  3C9M

  • PubMed Abstract: 
  • The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P3(1)) can be re-interpreted as hexagonal (space group P6(4)). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the ...

    The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P3(1)) can be re-interpreted as hexagonal (space group P6(4)). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the trigonal models. However, the noncrystallographic twofold axes parallel to the c axis can be treated as crystallographic symmetry operations in the hexagonal space group. This halves the asymmetric unit and makes all of the protein molecules equivalent in these structures. Corrections for merohedral twinning were also applied in the refinement in the higher symmetry space group for one of the structures (2j4y).


    Related Citations: 
    • Crystals of native and modified bovine rhodopsins and their heavy atom derivatives.
      Edwards, P.C.,Li, J.,Burghammer, M.,McDowell, J.H.,Villa, C.,Hargrave, P.A.,Schertler, G.F.
      (2004) J.Mol.Biol. 343: 1439
    • Structure of bovine rhodopsin in a trigonal crystal form.
      Li, J.,Edwards, P.C.,Burghammer, M.,Villa, C.,Schertler, G.F.
      (2004) J.Mol.Biol. 343: 1409


    Organizational Affiliation

    Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA. stenkamp@u.washington.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhodopsin
A
348Bos taurusGene Names: RHO
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Rhodopsin
Find proteins for P02699 (Bos taurus)
Go to Gene View: RHO
Go to UniProtKB:  P02699
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
C8E
Query on C8E

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A
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
PEF
Query on PEF

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A
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
RET
Query on RET

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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
LDA
Query on LDA

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A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

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A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
ACE
Query on ACE

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A
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.646 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 103.820α = 90.00
b = 103.820β = 90.00
c = 76.590γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-02-16 
  • Released Date: 2008-08-05 
  • Deposition Author(s): Stenkamp, R.E.

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2011-08-10
    Type: Other
  • Version 1.3: 2011-10-05
    Type: Other