1IW9
Crystal Structure of the M Intermediate of Bacteriorhodopsin
- PDB DOI: https://doi.org/10.2210/pdb1IW9/pdb
- Classification: PROTON TRANSPORT
- Organism(s): Halobacterium salinarum
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2002-04-25 Released: 2003-12-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.271 
- R-Value Work: 0.224 
- R-Value Observed: 0.224 
wwPDB Validation   3D Report Full Report
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 | 248 | Halobacterium salinarum | Mutation(s): 0  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 | |
L3P Query on L3P | D [auth A], F [auth A], G [auth A], H [auth A] | 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE C46 H94 O11 P2 TZXJQSKPTCRGCA-VZSPAKCESA-L | |||
L2P Query on L2P | E [auth A] | 2,3-DI-PHYTANYL-GLYCEROL C43 H88 O3 ISDBCJSGCHUHFI-UMZPFTBHSA-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: 2.50 Å
- R-Value Free: 0.271 
- R-Value Work: 0.224 
- R-Value Observed: 0.224 
- Space Group: P 6 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 102.3 | α = 90 |
b = 102.3 | β = 90 |
c = 112.3 | γ = 120 |
Software Name | Purpose |
---|---|
MOSFLM | data reduction |
SCALA | data scaling |
CNS | refinement |
CCP4 | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2003-12-23  Deposition Author(s): Takeda, K., Matsui, Y., Kamiya, N., Adachi, S., Okumura, H., Kouyama, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2003-12-23
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary