4G81 | pdb_00004g81

Crystal structure of a hexonate dehydrogenase ortholog (target efi-506402 from salmonella enterica, unliganded structure

PDB DOI: https://doi.org/10.2210/pdb4G81/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-20 Released: 2012-08-15
Deposition Author(s): Vetting, M.W., Wichelecki, D., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.164 (Depositor), 0.166 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a hexonate dehydrogenase ortholog (target efi-506402 from salmonella enterica, unliganded structure

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

To be published.

Macromolecule Content

Total Structure Weight: 109.86 kDa
Atom Count: 8,224
Modeled Residue Count: 1,012
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hexonate dehydrogenase	A [auth D], B [auth A], C [auth B], D [auth C]	255	Salmonella enterica subsp. enterica serovar Enteritidis str. P125109	Mutation(s): 0 Gene Names: SEN1435
UniProt
Find proteins for A0ABW1PX96 (Citrobacter bitternis) Explore A0ABW1PX96 Go to UniProtKB: A0ABW1PX96
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABW1PX96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain J [auth B] MOL2 format, chain E [auth D] MOL2 format, chain J [auth B] mmCIF format, chain E [auth D] mmCIF format, chain J [auth B]	E [auth D], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain J [auth B] Interactions & Density Focus chain E [auth D] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain F [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain F [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	F [auth D], H [auth B], I [auth B], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth D] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain F [auth D] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.202 (Depositor), 0.203 (DCC)
R-Value Work: 0.164 (Depositor), 0.166 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.65	α = 90
b = 94.197	β = 90
c = 129.356	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description