5MIW

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A.

PDB DOI: https://doi.org/10.2210/pdb5MIW/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-29 Released: 2017-12-20
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 ?
R-Value Free: 0.169
R-Value Work: 0.132
R-Value Observed: 0.133

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A.

Prokofev, I.I., Lashkov, A.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 164.99 kDa
Atom Count: 14,909
Modelled Residue Count: 1,509
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F	253	Vibrio cholerae	Mutation(s): 0 Gene Names: udp, udp_1 EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1 Go to UniProtKB: Q9K4U1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K4U1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URA Query on URA Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain LA [auth F] SDF format, chain O [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C]	DA [auth D] IA [auth E] J [auth A] LA [auth F] O [auth B] DA [auth D], IA [auth E], J [auth A], LA [auth F], O [auth B], W [auth C]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain IA [auth E] Focus chain J [auth A] Focus chain LA [auth F] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain IA [auth E] Focus chain J [auth A] Focus chain LA [auth F] Focus chain O [auth B] Focus chain W [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B]	K [auth A], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain K [auth A] Focus chain P [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain JA [auth E] SDF format, chain L [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	EA [auth D] FA [auth D] JA [auth E] L [auth A] MA [auth F] EA [auth D], FA [auth D], JA [auth E], L [auth A], MA [auth F], NA [auth F], Q [auth B], R [auth B], X [auth C], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain L [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain L [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C]	N [auth B], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain N [auth B] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth E] SDF format, chain KA [auth F] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	AA [auth D] BA [auth D] G [auth A] GA [auth E] KA [auth F] AA [auth D], BA [auth D], G [auth A], GA [auth E], KA [auth F], M [auth B], T [auth C], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	CA [auth D] H [auth A] HA [auth E] I [auth A] S [auth B] CA [auth D], H [auth A], HA [auth E], I [auth A], S [auth B], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain S [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 ?
R-Value Free: 0.169
R-Value Work: 0.132
R-Value Observed: 0.133
Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 64.513	α = 69.22
b = 71.948	β = 72.2
c = 89.332	γ = 85.6

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description