4W9Z | pdb_00004w9z

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
Deposition Author(s): Quade, N., Abicht, H.K., Hennecke, H., Glockshuber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.134 (Depositor), 0.151 (DCC)
R-Value Work:
0.109 (Depositor)
R-Value Observed:
0.110 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4W9Z

This is version 1.1 of the entry. See complete history.

Literature

Crystal 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.

Macromolecule Content

Total Structure Weight: 15.73 kDa
Atom Count: 1,378
Modeled Residue Count: 138
Deposited Residue Count: 139
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	A	139	Bradyrhizobium diazoefficiens USDA 110	Mutation(s): 0 Gene Names: coxB, blr1170 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H7C6E5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.134 (Depositor), 0.151 (DCC)
R-Value Work: 0.109 (Depositor)
R-Value Observed: 0.110 (Depositor)

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 Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
XSCALE	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.