1DZE
Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K
- PDB DOI: https://doi.org/10.2210/pdb1DZE/pdb
- Classification: BACTERIORHODOPSIN
- Organism(s): Halobacterium salinarum
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2000-02-25 Released: 2000-08-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.283 
- R-Value Work: 0.257 
- R-Value Observed: 0.257 
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 (M INTERMEDIATE) | 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 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
L3P Query on L3P | F [auth A] | 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE C46 H94 O11 P2 TZXJQSKPTCRGCA-VZSPAKCESA-L | |||
L4P Query on L4P | G [auth A] | 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL C46 H95 O8 P AFYVWQWWQKSZEV-WGOBCRBGSA-N | |||
L1P Query on L1P | D [auth A] | 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL C43 H89 O6 P UKQGAMWGTOTQPC-ALOLAALWSA-N | |||
L2P Query on L2P | E [auth A], H [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: 0.283 
- R-Value Work: 0.257 
- R-Value Observed: 0.257 
- Space Group: P 6 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 102.4 | α = 90 |
b = 102.4 | β = 90 |
c = 112.3 | γ = 120 |
Software Name | Purpose |
---|---|
X-PLOR | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 2000-08-16  Deposition Author(s): Takeda, K., Matsui, Y., Sato, H., Hino, T., Kanamori, E., Okumura, H., Yamane, T., Iizuka, T., Kamiya, N., Adachi, S., Kouyama, T.
Revision History (Full details and data files)
- Version 1.0: 2000-08-16
Type: Initial release - Version 1.1: 2011-05-07
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-12-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary