4WBJ | pdb_00004wbj

Crystal structure of Bradyrhizobium japonicum ScoI in the oxidized state

• PDB DOI: https://doi.org/10.2210/pdb4WBJ/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.104 (Depositor), 0.100 (DCC) 
• R-Value Observed: 
  0.106 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bradyrhizobium japonicum ScoI in the oxidized state

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 36.56 kDa 
• Atom Count: 3,039 
• Modeled Residue Count: 315 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blr1131 protein	A, B	164	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	C [auth A], D [auth B]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.104 (Depositor), 0.100 (DCC) 
• R-Value Observed: 0.106 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.776	α = 90
b = 82.629	β = 90.03
c = 45.853	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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary