3VHZ
Crystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin
- PDB DOI: https://doi.org/10.2210/pdb3VHZ/pdb
- Classification: PROTON TRANSPORT
- Organism(s): Halobacterium salinarum NRC-1
- Expression System: Halobacterium
- Mutation(s): Yes 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2011-09-13 Released: 2012-06-13 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.284 
- R-Value Observed: 0.252 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Bacteriorhodopsin | 262 | Halobacterium salinarum NRC-1 | Mutation(s): 1  Gene Names: bop, VNG_1467G Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P02945  Go to UniProtKB:  P02945 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P02945 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
L2P Query on L2P | E [auth A] | 2,3-DI-PHYTANYL-GLYCEROL C43 H88 O3 ISDBCJSGCHUHFI-UMZPFTBHSA-N | |||
SOG Query on SOG | D [auth A] | octyl 1-thio-beta-D-glucopyranoside C14 H28 O5 S CGVLVOOFCGWBCS-RGDJUOJXSA-N | |||
RET Query on RET | C [auth A] | RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.284 
- R-Value Observed: 0.252 
- Space Group: P 6 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 102.6 | α = 90 |
b = 102.6 | β = 90 |
c = 112.34 | γ = 120 |
Software Name | Purpose |
---|---|
ADSC | data collection |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2012-06-13  Deposition Author(s): Kouyama, T., Zhang, J.
Revision History (Full details and data files)
- Version 1.0: 2012-06-13
Type: Initial release - Version 1.1: 2014-04-23
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary