3TW9 | pdb_00003tw9

Crystal structure of gluconate dehydratase (TARGET EFI-501679) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109

PDB DOI: https://doi.org/10.2210/pdb3TW9/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: 1.70 Å
R-Value Free:
0.252 (Depositor), 0.253 (DCC)
R-Value Work:
0.211 (Depositor), 0.213 (DCC)
R-Value Observed:
0.212 (Depositor)

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 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: 196.93 kDa
Atom Count: 13,901
Modeled Residue Count: 1,607
Deposited Residue Count: 1,768
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dehydratase	A, B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5R541
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 E [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	E [auth A], I [auth B], L [auth C], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain Q [auth D]
CL Query on CL 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 J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.252 (Depositor), 0.253 (DCC)
R-Value Work: 0.211 (Depositor), 0.213 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.526	α = 90
b = 177.526	β = 90
c = 110.15	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description