5VN6 | pdb_00005vn6

Crystal structure of Taurine dioxygenase from Burkholderia ambifaria

• PDB DOI: https://doi.org/10.2210/pdb5VN6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia ambifaria MC40-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-28 Released: 2017-06-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Taurine dioxygenase from Burkholderia ambifaria

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

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.81 kDa 
• Atom Count: 4,486 
• Modeled Residue Count: 541 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Taurine dioxygenase	A, B	290	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_1605 EC: 1.14.11.17
UniProt
Find proteins for B1YQF4 (Burkholderia ambifaria (strain MC40-6)) Explore B1YQF4  Go to UniProtKB:  B1YQF4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VN6

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.18	α = 90
b = 84.89	β = 110.53
c = 95.68	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	model building
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description