3SDO | pdb_00003sdo

Structure of a Nitrilotriacetate monooxygenase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3SDO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-09 Released: 2011-06-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.213 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structure of a Nitrilotriacetate monooxygenase from Burkholderia pseudomallei

Clifton, M.C., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease, Sankaran, B.

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: 99.54 kDa 
• Atom Count: 6,879 
• Modeled Residue Count: 839 
• Deposited Residue Count: 906 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrilotriacetate monooxygenase	A, B	453	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: BURPS1710b_A1398 EC: 1.14.13
UniProt
Find proteins for Q3JIP8 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JIP8  Go to UniProtKB:  Q3JIP8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.213 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33SDO

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.187	α = 90
b = 92.783	β = 90
c = 162.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description