4JNQ | pdb_00004jnq

Crystal structure of a thioredoxin reductase from Brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb4JNQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brucella melitensis bv. 1 str. 16M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-15 Released: 2013-04-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.185 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a thioredoxin reductase from Brucella melitensis

Edwards, T.E., Arakaki, T.L., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 37.77 kDa 
• Atom Count: 2,603 
• Modeled Residue Count: 315 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A	345	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0  Gene Names: BAWG_2493, BMEI0512 EC: 1.8.1.9
UniProt
Find proteins for Q8YID2 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YID2  Go to UniProtKB:  Q8YID2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA	B [auth A]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.185 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34JNQ

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.79	α = 90
b = 77.19	β = 90
c = 104.08	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary