3TWB | pdb_00003twb

Crystal structure of gluconate dehydratase (TARGET EFI-501679) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 complexed with magnesium and gluconic acid

PDB DOI: https://doi.org/10.2210/pdb3TWB/pdb

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

Deposited: 2011-09-21 Released: 2011-10-26
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Gluconate Dehydratase from Salmonella Enterica P125109

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 247.07 kDa
Atom Count: 18,525
Modelled Residue Count: 2,079
Deposited Residue Count: 2,210
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dehydratase	A, B, C, D, E	442	Salmonella enterica subsp. enterica serovar Enteritidis str. P125109	Mutation(s): 0 Gene Names: SEN1436 EC: 4.2.1 (UniProt), 4.2.1.39 (UniProt)
UniProt
Find proteins for B5R541 (Salmonella enteritidis PT4 (strain P125109)) Explore B5R541 Go to UniProtKB: B5R541
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5R541
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCO Query on GCO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	I [auth A], M [auth B], R [auth C], U [auth D], Y [auth E]	D-gluconic acid C₆ H₁₂ O₇ RGHNJXZEOKUKBD-SQOUGZDYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain V [auth D] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth D] MOL2 format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth D] mmCIF format, chain J [auth A]	G [auth A] J [auth A] L [auth B] O [auth C] Q [auth C] G [auth A], J [auth A], L [auth B], O [auth C], Q [auth C], T [auth D], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain V [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth C] SDF format, chain X [auth E] MOL2 format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain X [auth E] mmCIF format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain X [auth E]	H [auth A], P [auth C], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain P [auth C] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain P [auth C] Focus chain X [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] SDF format, chain F [auth A] SDF format, chain W [auth E] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain W [auth E] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain W [auth E]	F [auth A], K [auth B], N [auth C], S [auth D], W [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain W [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.727	α = 90
b = 144.727	β = 90
c = 446.996	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2012-03-07
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary