4NIM | pdb_00004nim

Crystal Structure of a Short Chain Dehydrogenase from Brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb4NIM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brucella melitensis ATCC 23457
• Mutation(s): No 


• Deposited: 2013-11-06 Released: 2013-11-20 
• Deposition Author(s): Dranow, D.M., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Short Chain Dehydrogenase from Brucella melitensis

Dranow, D.M., Edwards, T.E., Lorimer, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.11 kDa 
• Atom Count: 1,973 
• Modeled Residue Count: 240 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Versicolorin reductase	A	277	Brucella melitensis ATCC 23457	Mutation(s): 0  Gene Names: BMEA_A1386
UniProt
Find proteins for C0RJU5 (Brucella melitensis biotype 2 (strain ATCC 23457)) Explore C0RJU5  Go to UniProtKB:  C0RJU5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34NIM

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.21	α = 90
b = 118.21	β = 90
c = 85.18	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: 2013-11-20 
Deposition Author(s): Dranow, D.M., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Structure summary
• Version 1.2: 2015-09-16
  Changes: Other, Structure summary
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description