5U4S

Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP.

• PDB DOI: https://doi.org/10.2210/pdb5U4S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-06 Released: 2017-01-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.166 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Literature

Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP

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)

Macromolecule Content

• Total Structure Weight: 53.87 kDa 
• Atom Count: 4,038 
• Modelled Residue Count: 467 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative short chain dehydrogenase	A, B	245	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: BCAM2128
UniProt
Find proteins for B4EFS5 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EFS5  Go to UniProtKB:  B4EFS5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
BEZ	D [auth A], G [auth B]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.166 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M35U4S

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.27	α = 90
b = 75.66	β = 90
c = 146.01	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references