4E7C

E. cloacae MurA in complex with UTP

PDB DOI: https://doi.org/10.2210/pdb4E7C/pdb

Classification: TRANSFERASE
Organism(s): Enterobacter cloacae subsp. cloacae ATCC 13047
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-16 Released: 2013-03-20
Deposition Author(s): Zhu, J.-Y., Yang, Y., Schonbrunn, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Open-close transition of MurA

Zhu, J.-Y., Yang, Y., Betzi, S., Schonbrunn, E.

To be published.

Macromolecule Content

Total Structure Weight: 181.38 kDa
Atom Count: 13,738
Modelled Residue Count: 1,676
Deposited Residue Count: 1,676
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A, B, C, D	419	Enterobacter cloacae subsp. cloacae ATCC 13047	Mutation(s): 0 Gene Names: ECL_04571, murA, murZ EC: 2.5.1.7
UniProt
Find proteins for P33038 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56)) Explore P33038 Go to UniProtKB: P33038
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33038
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UTP Query on UTP Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B]	J [auth A], M [auth B]	URIDINE 5'-TRIPHOSPHATE C₉ H₁₅ N₂ O₁₅ P₃ PGAVKCOVUIYSFO-XVFCMESISA-N		Interactions Focus chain J [auth A] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	E [auth A] F [auth A] G [auth A] K [auth B] N [auth C] E [auth A], F [auth A], G [auth A], K [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	H [auth A] I [auth A] L [auth B] S [auth C] W [auth D] H [auth A], I [auth A], L [auth B], S [auth C], W [auth D], X [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.94	α = 90
b = 101.27	β = 90
c = 213.67	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
CNS	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Zhu, J.-Y.

Yang, Y.

Schonbrunn, E.

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary