Download MendeleyCrystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2OUW
Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2OUW/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Rhodospirillum rubrum
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-02-12 Released: 2007-03-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.232
- R-Value Work: 0.195
- R-Value Observed: 0.197
wwPDB Validation 3D Report Full Report
This is version 1.5 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Alkylhydroperoxidase AhpD core | 138 | Rhodospirillum rubrum | Mutation(s): 5 Gene Names: YP_425393.1, Rru_A0301 EC: 1 |  | |
UniProt | |||||
Find proteins for Q2RXN9 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RXN9 Go to UniProtKB: Q2RXN9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2RXN9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACY Query on ACY | E [auth A], F [auth A], H [auth B], I [auth B] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| NA Query on NA | C [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | D [auth A], G [auth B] | Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N | |||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.232
- R-Value Work: 0.195
- R-Value Observed: 0.197
- Space Group: P 63 2 2
- Diffraction Data: https://doi.org/10.18430/M32OUW
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 62.683 | α = 90 |
| b = 62.683 | β = 90 |
| c = 216.707 | γ = 120 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| SHELX | phasing |
| REFMAC | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHARP | phasing |
Entry History
Deposition Data
- Released Date: 2007-03-06 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-03-06
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2017-10-25
Changes: Author supporting evidence - Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
