4WBR | pdb_00004wbr

Structure of Bradyrhizobium japonicum ScoI with copper bound

PDB DOI: https://doi.org/10.2210/pdb4WBR/pdb

Classification: CHAPERONE
Organism(s): Bradyrhizobium diazoefficiens USDA 110
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-03 Released: 2015-09-23
Deposition Author(s): Quade, N., Abicht, H.K., Hennecke, H., Glockshuber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.175 (Depositor), 0.176 (DCC)
R-Value Work:
0.126 (Depositor), 0.126 (DCC)
R-Value Observed:
0.128 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of Bradyrhizobium japonicum ScoI with copper bound

Quade, N., Abicht, H.K., Hennecke, H., Glockshuber, R.

To be published.

Macromolecule Content

Total Structure Weight: 17.5 kDa
Atom Count: 1,504
Modeled Residue Count: 157
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blr1131 protein	A [auth D]	157	Bradyrhizobium diazoefficiens USDA 110	Mutation(s): 0 Gene Names: blr1131
UniProt
Find proteins for Q89VB6 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89VB6 Go to UniProtKB: Q89VB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89VB6
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 B [auth D] MOL2 format, chain B [auth D] mmCIF format, chain B [auth D]	B [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth D] Interactions & Density Focus chain B [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.175 (Depositor), 0.176 (DCC)
R-Value Work: 0.126 (Depositor), 0.126 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.86	α = 90
b = 44.76	β = 90
c = 40	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-09-23

Deposition Author(s):

Glockshuber, R.

Revision History (Full details and data files)

Version 1.0: 2015-09-23
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.