4OGL | pdb_00004ogl

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb4OGL/pdb

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

Deposited: 2014-01-16 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: 1.25 ?
R-Value Free:
0.147 (Depositor), 0.150 (DCC)
R-Value Work:
0.115 (Depositor), 0.110 (DCC)
R-Value Observed:
0.117 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution

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

(2016) Crystallogr Rep

DOI: https://doi.org/10.1134/S1063774516060134

Macromolecule Content

Total Structure Weight: 164.71 kDa
Atom Count: 14,803
Modeled Residue Count: 1,502
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 Q9KT71 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KT71 Go to UniProtKB: Q9KT71
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KT71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TDR Query on TDR Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain W [auth E] SDF format, chain N [auth C] SDF format, chain T [auth D] MOL2 format, chain BA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain W [auth E] MOL2 format, chain N [auth C] MOL2 format, chain T [auth D] mmCIF format, chain BA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain W [auth E] mmCIF format, chain N [auth C] mmCIF format, chain T [auth D]	BA [auth F] G [auth A] K [auth B] N [auth C] T [auth D] BA [auth F], G [auth A], K [auth B], N [auth C], T [auth D], W [auth E]	THYMINE C₅ H₆ N₂ O₂ RWQNBRDOKXIBIV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain BA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain W [auth E]
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		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 EA [auth F] SDF format, chain I [auth A] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain Z [auth E] SDF format, chain V [auth D] MOL2 format, chain EA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] mmCIF format, chain EA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D]	EA [auth F] I [auth A] R [auth C] U [auth D] V [auth D] EA [auth F], I [auth A], R [auth C], U [auth D], V [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain I [auth A] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain I [auth A] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Z [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain X [auth E] SDF format, chain DA [auth F] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain Y [auth E]	CA [auth F] DA [auth F] H [auth A] L [auth B] O [auth C] CA [auth F], DA [auth F], H [auth A], L [auth B], O [auth C], P [auth C], Q [auth C], X [auth E], Y [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain X [auth E] Focus chain Y [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain J [auth A] SDF format, chain S [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain S [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain S [auth C]	AA [auth E], J [auth A], S [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain J [auth A] Focus chain S [auth C] Interactions & Density Focus chain AA [auth E] Focus chain J [auth A] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 ?
R-Value Free: 0.147 (Depositor), 0.150 (DCC)
R-Value Work: 0.115 (Depositor), 0.110 (DCC)
R-Value Observed: 0.117 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 92.748	α = 90
b = 96.499	β = 119.99
c = 92.776	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
XDS	data reduction
PHASER	phasing

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: 2017-01-11
Changes: Database references
Version 1.2: 2018-01-17
Changes: Data collection
Version 1.3: 2018-03-07
Changes: Data collection
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description