3C9M

Structure of a mutant bovine rhodopsin in hexagonal crystal form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in:2J4Y


Literature

Alternative models for two crystal structures of bovine rhodopsin.

Stenkamp, R.E.

(2008) Acta Crystallogr D Biol Crystallogr 64: 902-904

  • DOI: 10.1107/S0907444908017162
  • Primary Citation of Related Structures:  
    3C9L, 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: 
    • Crystal structure of a thermally stable rhodopsin mutant
      Standfuss, J., Xie, G., Edwards, P.C., Burghammer, M., Oprian, D.D., Schertler, G.F.
      (2007) J Mol Biol 372: 1179
    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RhodopsinA348Bos taurusMutation(s): 2 
Gene Names: RHO
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET
Download Ideal Coordinates CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
ACE
Query on ACE
Download Ideal Coordinates CCD File 
A
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.3α = 90
b = 109.3β = 90
c = 77.7γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

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View more in-depth experimental data

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
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Other
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary