3E99

Crystal structure of the beta subunit of the benzoate 1,2-dioxygenase (benb, bmaa0186) from burkholderia mallei atcc 23344 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3E99/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia mallei ATCC 23344
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-21 Released: 2008-09-16 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Crystal structure of the beta subunit of benzoate 1,2-dioxygenase (YP_105014.1) from BURKHOLDERIA MALLEI ATCC 23344 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 19.41 kDa 
• Atom Count: 1,422 
• Modelled Residue Count: 149 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoate 1,2-dioxygenase beta subunit	A	164	Burkholderia mallei ATCC 23344	Mutation(s): 0  Gene Names: YP_105014.1, benB, BMAA0186 EC: 1.14.12.10
UniProt
Find proteins for A0A0H2WBM4 (Burkholderia mallei (strain ATCC 23344)) Explore A0A0H2WBM4  Go to UniProtKB:  A0A0H2WBM4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 6₃ 2 2
• Diffraction Data: https://doi.org/10.18430/M33E99

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.953	α = 90
b = 58.953	β = 90
c = 167.073	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations