4KZP

Crystal Structure of a Putative Short Chain Dehydrogenase from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb4KZP/pdb

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

Deposited: 2013-05-30 Released: 2013-07-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.205
R-Value Work: 0.176
R-Value Observed: 0.178

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of a Putative Short Chain Dehydrogenase from Mycobacterium smegmatis

Dranow, D.M., Fairman, J.W., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 132.52 kDa
Atom Count: 9,616
Modelled Residue Count: 1,161
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short chain dehydrogenase/reductase family protein	A, B, C, D	320	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEG_5903, MSMEI_5743 EC: 1.1.1.100
UniProt
Find proteins for A0R4P1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R4P1 Go to UniProtKB: A0R4P1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R4P1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain K [auth A] SDF format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain K [auth A] MOL2 format, chain U [auth D]	K [auth A], Q [auth C], R [auth C], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain K [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth C], N [auth C], O [auth C], P [auth C], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.205
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M34KZP

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.7	α = 90
b = 86.07	β = 103.4
c = 92.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description