4LZW

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymidine at 1.29 A resolution

PDB DOI: https://doi.org/10.2210/pdb4LZW/pdb

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

Deposited: 2013-08-01 Released: 2014-12-31
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: 1.29 Å
R-Value Free: 0.210
R-Value Work: 0.178
R-Value Observed: 0.179

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

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., Gabdoulkhakov, A.G., Balaev, V.V., Seregina, T.A., Mironov, A.S., Betzel, C., Mikhailov, A.M.

(2016) Crystallogr Rep

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

Macromolecule Content

Total Structure Weight: 165.08 kDa
Atom Count: 14,145
Modelled Residue Count: 1,495
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	Mutation(s): 0 Gene Names: udp 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
THM Query on THM Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain G [auth A] SDF format, chain IA [auth F] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	DA [auth E] G [auth A] IA [auth F] N [auth B] S [auth C] DA [auth E], G [auth A], IA [auth F], N [auth B], S [auth C], Y [auth D]	THYMIDINE C₁₀ H₁₄ N₂ O₅ IQFYYKKMVGJFEH-XLPZGREQSA-N		Interactions Focus chain DA [auth E] Focus chain G [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain G [auth A] Focus chain IA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain T [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain T [auth C] mmCIF format, chain EA [auth E] mmCIF format, chain T [auth C]	EA [auth E], T [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain T [auth C] Interactions & Density Focus chain EA [auth E] Focus chain T [auth C]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth F] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth D]	FA [auth E] H [auth A] I [auth A] JA [auth F] O [auth B] FA [auth E], H [auth A], I [auth A], JA [auth F], O [auth B], P [auth B], Z [auth D]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain GA [auth E] SDF format, chain J [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain MA [auth F] SDF format, chain Q [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C]	AA [auth D] GA [auth E] J [auth A] KA [auth F] L [auth A] AA [auth D], GA [auth E], J [auth A], KA [auth F], L [auth A], MA [auth F], Q [auth B], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain U [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain HA [auth E] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	BA [auth D] CA [auth D] HA [auth E] M [auth A] R [auth B] BA [auth D], CA [auth D], HA [auth E], M [auth A], R [auth B], W [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain HA [auth E] Focus chain M [auth A] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain HA [auth E] Focus chain M [auth A] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain LA [auth F] SDF format, chain V [auth C] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain V [auth C] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain V [auth C]	K [auth A], LA [auth F], V [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain LA [auth F] Focus chain V [auth C] Interactions & Density Focus chain K [auth A] Focus chain LA [auth F] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.210
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.74	α = 90
b = 95.85	β = 119.96
c = 91.83	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-31
Type: Initial release
Version 1.1: 2016-12-28
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description