5U8P | pdb_00005u8p

Crystal structure of a short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb5U8P/pdb

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


• Deposited: 2016-12-14 Released: 2017-02-15 
• 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: 
  0.137 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.117 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD

Abendroth, J., Delker, S.L., 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: 66.61 kDa 
• Atom Count: 5,413 
• Modeled Residue Count: 584 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B	310	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: BCAL1205
UniProt
Find proteins for B4EEE3 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EEE3  Go to UniProtKB:  B4EEE3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.137 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.117 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35U8P

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.16	α = 90
b = 103.08	β = 120.68
c = 87	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description