4R7U

Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Vibrio cholerae in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin

PDB DOI: https://doi.org/10.2210/pdb4R7U/pdb

Classification: TRANSFERASE/ANTIBIOTIC
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-28 Released: 2014-09-24
Deposition Author(s): Nocek, B., Maltseva, N., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.234 (Depositor), 0.237 (DCC)
R-Value Work:
0.178 (Depositor), 0.181 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Vibrio cholerae in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin

Nocek, B., Maltseva, N., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 183.35 kDa
Atom Count: 12,961
Modelled Residue Count: 1,673
Deposited Residue Count: 1,688
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A, B, C, D	422	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: murA, VC_2514 EC: 2.5.1.7
UniProt
Find proteins for Q9KP62 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KP62 Go to UniProtKB: Q9KP62
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KP62
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD1 Query on UD1 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	G [auth A], I [auth B], L [auth C], P [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-CFRASDGPSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FFQ Query on FFQ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	F [auth A], J [auth B], M [auth C], Q [auth D]	[(1R)-1-hydroxypropyl]phosphonic acid C₃ H₉ O₄ P MVIJUJBSAAUHEM-GSVOUGTGSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	H [auth A], K [auth B], N [auth C], O [auth C], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.234 (Depositor), 0.237 (DCC)
R-Value Work: 0.178 (Depositor), 0.181 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34r7u

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.283	α = 90
b = 204.283	β = 90
c = 118.878	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary