2ZOO
Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125
- PDB DOI: https://doi.org/10.2210/pdb2ZOO/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Pseudoalteromonas translucida TAC125
- Mutation(s): No
- Deposited: 2008-05-27 Released: 2009-06-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.186
- R-Value Work: 0.166
- R-Value Observed: 0.168
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 |
| Probable nitrite reductase | 442 | Pseudoalteromonas translucida TAC125 | Mutation(s): 0 EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (PDB Primary Data) |  | |
UniProt | |||||
Find proteins for Q3IGF7 (Pseudoalteromonas translucida (strain TAC 125)) Explore Q3IGF7 Go to UniProtKB: Q3IGF7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q3IGF7 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEM Query on HEM | E [auth A] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | ||
| SO4 Query on SO4 | F [auth A], G [auth A], H [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| CU Query on CU | C [auth A], D [auth A] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900003 Query on PRD_900003 | B | sucrose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.186
- R-Value Work: 0.166
- R-Value Observed: 0.168
- Space Group: P 41 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 180.338 | α = 90 |
| b = 180.338 | β = 90 |
| c = 180.338 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2009-06-09 Deposition Author(s): Nojiri, M., Tsuda, A., Yamaguchi, K., Suzuki, S.
Revision History (Full details and data files)
- Version 1.0: 2009-06-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
