4GVX | pdb_00004gvx

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

PDB DOI: https://doi.org/10.2210/pdb4GVX/pdb

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

Deposited: 2012-08-31 Released: 2012-10-03
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: 1.50 Å
R-Value Free:
0.179 (Depositor), 0.179 (DCC)
R-Value Work:
0.152 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (Depositor)

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 homolog (target EFI-505321) from burkholderia multivorans, with bound NADP and L-fucose

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: 115.07 kDa
Atom Count: 9,232
Modeled Residue Count: 1,032
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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| 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: BMULJ_04919, Bmul_3598, fabG 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3KNE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	E [auth A], K [auth B], P [auth C], T [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]
FUL Query on FUL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	G [auth A], N [auth B], R [auth C], V [auth D]	beta-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-KGJVWPDLSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] M [auth B] O [auth B] S [auth C] I [auth A], J [auth A], M [auth B], O [auth B], S [auth C], W [auth D], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D]	F [auth A], L [auth B], Q [auth C], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.179 (Depositor), 0.179 (DCC)
R-Value Work: 0.152 (Depositor), 0.152 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.437	α = 90
b = 118.522	β = 92.92
c = 118.283	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-10-03

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-10-03
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary