Download MendeleyCrystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum
Quade, N., Abicht, H.K., Hennecke, H., Glockshuber, R.To be published.
4W9Z
Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum
- PDB DOI: https://doi.org/10.2210/pdb4W9Z/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Bradyrhizobium diazoefficiens USDA 110
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-08-28 Released: 2015-09-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.134
- R-Value Work: 0.109
- R-Value Observed: 0.110
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| Cytochrome c oxidase subunit 2 | 139 | Bradyrhizobium diazoefficiens USDA 110 | Mutation(s): 0 Gene Names: coxB, blr1170 EC: 1.9.3.1 |  | |
UniProt | |||||
Find proteins for H7C6E5 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore H7C6E5 Go to UniProtKB: H7C6E5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | H7C6E5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CU Query on CU | B [auth A], C [auth A] | COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.134
- R-Value Work: 0.109
- R-Value Observed: 0.110
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 32.431 | α = 90 |
| b = 38.612 | β = 97.63 |
| c = 59.644 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Coot | model building |
| PDB_EXTRACT | data extraction |
| XSCALE | data scaling |
| PHASER | phasing |
| XSCALE | data reduction |
Entry History
Deposition Data
- Released Date: 2015-09-09 Deposition Author(s): Quade, N., Abicht, H.K., Hennecke, H., Glockshuber, R.
Revision History (Full details and data files)
- Version 1.0: 2015-09-09
Type: Initial release - Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
