3EMK | pdb_00003emk

2.5A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb3EMK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brucella melitensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-24 Released: 2008-10-28 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

2.5A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 104.3 kDa 
• Atom Count: 7,138 
• Modeled Residue Count: 947 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSE/RIBITOL DEHYDROGENASE	A, B, C, D	246	Brucella melitensis	Mutation(s): 0  Gene Names: BMEI1477 EC: 1.1.1.100
UniProt
Find proteins for Q2YMG6 (Brucella abortus (strain 2308)) Explore Q2YMG6  Go to UniProtKB:  Q2YMG6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.489	α = 90
b = 147.939	β = 90
c = 63.892	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references