4E7B | pdb_00004e7b

E. cloacae MurA in complex with UDP-glucose

PDB DOI: https://doi.org/10.2210/pdb4E7B/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: 2.00 ?
R-Value Free:
0.226 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
View more details

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: 184.31 kDa
Atom Count: 14,068
Modeled 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
UPG Query on UPG Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain Q [auth A] SDF format, chain UA [auth C] SDF format, chain ZA [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain ZA [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain ZA [auth D]	GA [auth B], Q [auth A], UA [auth C], ZA [auth D]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain GA [auth B] Focus chain Q [auth A] Focus chain UA [auth C] Focus chain ZA [auth D] Interactions & Density Focus chain GA [auth B] Focus chain Q [auth A] Focus chain UA [auth C] Focus chain ZA [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain R [auth B] SDF format, chain RA [auth C] SDF format, chain S [auth B] SDF format, chain SA [auth C] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain QA [auth C] SDF format, chain VA [auth D] SDF format, chain WA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], PA [auth C], QA [auth C], R [auth B], RA [auth C], S [auth B], SA [auth C], T [auth B], U [auth B], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain R [auth B] Focus chain RA [auth C] Focus chain S [auth B] Focus chain SA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain TA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain TA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain TA [auth C]	P [auth A], TA [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth A] Focus chain TA [auth C] Interactions & Density Focus chain P [auth A] Focus chain TA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.226 (Depositor), 0.220 (DCC)
R-Value Work: 0.186 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 78.11	α = 90
b = 103.22	β = 90
c = 218.95	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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: 2024-10-09
Changes: Structure summary