4WEC

Crystal structure of a Short chain dehydrogenase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb4WEC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-09 Released: 2014-10-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.196 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Crystal structure of a Short chain dehydrogenase from Mycobacterium smegmatis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Sankaran, B., Dranow, D.M., Lorimer, 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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 119.94 kDa 
• Atom Count: 8,762 
• Modelled Residue Count: 1,023 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D	278	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_2598, MSMEI_2536
UniProt
Find proteins for A0QVJ7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QVJ7  Go to UniProtKB:  A0QVJ7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], J [auth B], O [auth C], R [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	F [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], L [auth B], N [auth B], Q [auth C], T [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	G [auth A], K [auth B], P [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.196 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34WEC

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.9	α = 90
b = 96.64	β = 101.94
c = 81.54	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Advisory, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description