4GLO | pdb_00004glo

Crystal structure of a short chain dehydrogenase homolog (target EFI-505321) from burkholderia multivorans, with bound NAD

PDB DOI: https://doi.org/10.2210/pdb4GLO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia multivorans ATCC 17616
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-08-14 Released: 2012-08-29
Deposition Author(s): Vetting, M.W., Hobbs, M.E., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.150 (Depositor), 0.150 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a short chain dehydrogenase homolog (target EFI-505321) from burkholderia multivorans, with bound NAD

Vetting, M.W., Hobbs, M.E., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 115 kDa
Atom Count: 8,895
Modeled Residue Count: 1,014
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier protein] reductase	A, B, C, D	258	Burkholderia multivorans ATCC 17616	Mutation(s): 0 Gene Names: fabG, Bmul_3598, BMULJ_04919 EC: 1.1.1.100 (PDB Primary Data), 1.1.1.435 (UniProt)
UniProt
Find proteins for A0A0H3KNE7 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KNE7 Go to UniProtKB: A0A0H3KNE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3KNE7
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 L [auth B] SDF format, chain Q [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth D]	E [auth A], L [auth B], Q [auth C], X [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	F [auth A] G [auth A] H [auth A] M [auth B] N [auth B] F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], R [auth C], S [auth C], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	BA [auth D] CA [auth D] J [auth A] K [auth A] P [auth B] BA [auth D], CA [auth D], J [auth A], K [auth A], P [auth B], U [auth C], V [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C]	AA [auth D], I [auth A], O [auth B], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.181 (Depositor), 0.180 (DCC)
R-Value Work: 0.150 (Depositor), 0.150 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.59	α = 90
b = 99.59	β = 90
c = 206.389	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description