3C9L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Re-refinement Note

This entry reflects an alternative modeling of the original data in:1GZM


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: 
    • 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
    • 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

    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): 0 
Gene Names: RHO
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEF
Query on PEF

Download Ideal Coordinates CCD File 
A
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
C8E
Query on C8E

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

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

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A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-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
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-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: 2.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.82α = 90
b = 103.82β = 90
c = 76.59γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report



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: 2011-08-10
    Changes: Other
  • Version 1.3: 2011-10-05
    Changes: Other
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary