6H5D | pdb_00006h5d

Crystal structure of DHQ1 from Salmonella typhi covalently modified by ligand 2

PDB DOI: https://doi.org/10.2210/pdb6H5D/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-24 Released: 2019-07-24
Deposition Author(s): Sanz-Gaitero, M., Maneiro, M., Lence, E., Otero, J.M., Thompson, P., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.200 (Depositor), 0.207 (DCC)
R-Value Work:
0.158 (Depositor)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Hydroxylammonium Derivatives for Selective Active-site Lysine Modification in the Anti-virulence Bacterial Target DHQ1 Enzyme.

Maneiro, M., Lence, E., Sanz-Gaitero, M., Otero, J.M., van Raaij, M.J., Thompson, P., Hawkins, A.R., Gonzalez-Bello, C.

(2019) Org Chem Front 9: 3127-3135

DOI: https://doi.org/10.1039/c9qo00453j

Macromolecule Content

Total Structure Weight: 55.74 kDa
Atom Count: 4,841
Modeled Residue Count: 504
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B	252	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0 Gene Names: aroD, STY1760, t1231 EC: 4.2.1.10
UniProt
Find proteins for P24670 (Salmonella typhi) Explore P24670 Go to UniProtKB: P24670
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24670
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WPL (Subject of Investigation/LOI) Query on WPL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(1~{S},3~{S},4~{R},5~{R})-3-methyl-1,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid C₈ H₁₄ O₅ NMVUNDOHFYILSF-FJDLHZNMSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.200 (Depositor), 0.207 (DCC)
R-Value Work: 0.158 (Depositor)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.219	α = 90
b = 44.057	β = 95.25
c = 84.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BFU2014-53425-P

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 1.1: 2019-08-07
Changes: Data collection, Database references, Structure summary
Version 1.2: 2019-08-28
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2019-10-09
Changes: Data collection, Database references
Version 1.4: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-11-20
Changes: Structure summary