4OEH

X-ray Structure of Uridine Phosphorylase from Vibrio cholerae Complexed with Uracil at 1.91 A Resolution

PDB DOI: https://doi.org/10.2210/pdb4OEH/pdb

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

Deposited: 2014-01-13 Released: 2015-03-04
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.216
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases.

Prokofev, I.I., Lashkov, A.A., Balaev, T., Seregina, A.S., Mironov, C., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 164.31 kDa
Atom Count: 12,849
Modelled Residue Count: 1,506
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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(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 O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: udp, VC_1034 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 K [auth B] SDF format, chain X [auth F] SDF format, chain G [auth A] SDF format, chain U [auth E] MOL2 format, chain K [auth B] MOL2 format, chain X [auth F] MOL2 format, chain G [auth A] MOL2 format, chain U [auth E] mmCIF format, chain K [auth B] mmCIF format, chain X [auth F] mmCIF format, chain G [auth A] mmCIF format, chain U [auth E]	G [auth A], K [auth B], U [auth E], X [auth F]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain U [auth E] Focus chain X [auth F]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	H [auth A] L [auth B] O [auth C] R [auth D] V [auth E] H [auth A], L [auth B], O [auth C], R [auth D], V [auth E], Y [auth F], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Y [auth F] Focus chain Z [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain W [auth E] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth E] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth E]	I [auth A], P [auth C], Q [auth C], W [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth E] Interactions & Density Focus chain I [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain W [auth E]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain J [auth A] SDF format, chain S [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain S [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain S [auth D]	AA [auth F], J [auth A], S [auth D]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain J [auth A] Focus chain S [auth D] Interactions & Density Focus chain AA [auth F] Focus chain J [auth A] Focus chain S [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain N [auth B] SDF format, chain T [auth D] MOL2 format, chain BA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain T [auth D] mmCIF format, chain BA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain T [auth D]	BA [auth F], N [auth B], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain N [auth B] Focus chain T [auth D] Interactions & Density Focus chain BA [auth F] Focus chain N [auth B] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.216
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.255	α = 69.14
b = 71.763	β = 72.15
c = 89.321	γ = 85.79

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 1.1: 2015-03-11
Changes: Other
Version 1.2: 2017-01-11
Changes: Database references
Version 1.3: 2018-01-17
Changes: Data collection, Database references, Refinement description
Version 1.4: 2018-03-07
Changes: Data collection
Version 1.5: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description