5IG2 | pdb_00005ig2

Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb5IG2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paraburkholderia phymatum STM815
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-26 Released: 2016-06-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum in complex with NAD

Mayclin, S.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 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.97 kDa 
• Atom Count: 7,208 
• Modeled Residue Count: 838 
• Deposited Residue Count: 891 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B, C	297	Paraburkholderia phymatum STM815	Mutation(s): 0  Gene Names: Bphy_1038
UniProt
Find proteins for B2JGP2 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JGP2  Go to UniProtKB:  B2JGP2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], F [auth B], H [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ACT	E [auth A], G [auth B], I [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IG2

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.52	α = 90
b = 187.79	β = 90
c = 108.26	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description