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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QVJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	E [auth A], J [auth B], O [auth C], R [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain R [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	H [auth A] I [auth A] L [auth B] N [auth B] Q [auth C] 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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	G [auth A], K [auth B], P [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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