4E6M | pdb_00004e6m

Crystal structure of Putative dehydratase protein from Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella typhimurium)

PDB DOI: https://doi.org/10.2210/pdb4E6M/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-15 Released: 2012-04-04
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Zenchek, W., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (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 Putative dehydratase protein from Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella typhimurium)

Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Zenchek, W., Love, J., Fiser, A., Khafizov, K., Seidel, R., Bonanno, J.B., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 380.77 kDa
Atom Count: 27,937
Modeled Residue Count: 3,208
Deposited Residue Count: 3,384
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dehydratase protein	A, B, C, D, E A, B, C, D, E, F, G, H	423	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: STM2273
UniProt
Find proteins for Q8ZNH1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNH1 Go to UniProtKB: Q8ZNH1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZNH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain HA [auth H] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain DA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain DA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain DA [auth G]	DA [auth G] HA [auth H] N [auth B] O [auth B] R [auth C] DA [auth G], HA [auth H], N [auth B], O [auth B], R [auth C], U [auth D], X [auth E], Y [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Focus chain HA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain DA [auth G] Focus chain HA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain GA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain K [auth A] SDF format, chain CA [auth G] SDF format, chain AA [auth F] MOL2 format, chain EA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain EA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] CA [auth G] EA [auth H] GA [auth H] J [auth A] AA [auth F], CA [auth G], EA [auth H], GA [auth H], J [auth A], K [auth A], M [auth B], Q [auth C], T [auth D], W [auth E]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain GA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain Z [auth F] SDF format, chain V [auth E] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain FA [auth H] MOL2 format, chain BA [auth G] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth E] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth H] mmCIF format, chain BA [auth G] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth E] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth H]	BA [auth G] FA [auth H] I [auth A] L [auth B] P [auth C] BA [auth G], FA [auth H], I [auth A], L [auth B], P [auth C], S [auth D], V [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain FA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.173 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.128	α = 90
b = 87.137	β = 91.39
c = 200.586	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-04-04

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-04-04
Type: Initial release
Version 1.1: 2012-05-09
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description