5IZ4 | pdb_00005iz4

Crystal structure of a putative short-chain dehydrogenase/reductase from Burkholderia xenovorans

• PDB DOI: https://doi.org/10.2210/pdb5IZ4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-24 Released: 2016-05-04 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.182 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative short-chain dehydrogenase/reductase from Burkholderia xenovorans

Abendroth, J., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

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: 29.07 kDa 
• Atom Count: 2,116 
• Modeled Residue Count: 247 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative short-chain dehydrogenase/reductase	A	271	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: Bxe_C0900 EC: 1.1.1.100
UniProt
Find proteins for Q13GL4 (Paraburkholderia xenovorans (strain LB400)) Explore Q13GL4  Go to UniProtKB:  Q13GL4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MRD	C [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.182 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IZ4

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.61	α = 90
b = 84.61	β = 90
c = 135.25	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description