6RCA

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 2.2'-anhydrouridine at 1.34 A

PDB DOI: https://doi.org/10.2210/pdb6RCA/pdb
Entry: 6RCA supersedes: 5OUR

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

Deposited: 2019-04-11 Released: 2020-05-13
Deposition Author(s): Prokofev, I.I., Eistrikh-Geller, P.A., Balaev, V.V., Gabdoulkhakov, A.G., Betzel, C., Lashkov, A.A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.169
R-Value Work: 0.135
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5OUR

Literature

X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine

Eistrikh-Geller, P.A., Rubinsky, S.V., Prokofev, I.I., Gabdoulkhakov, A.G., Mironov, A.S., Lashkov, A.A.

(2020) Crystallogr Rep

DOI: https://doi.org/10.1134/S1063774520020066

Macromolecule Content

Total Structure Weight: 164.97 kDa
Atom Count: 14,891
Modelled Residue Count: 1,508
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, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055... udp, udp_1, B2J67_05455, B2J68_05210, B2J71_05165, BFX32_04820, BTY66_05555, CEF09_03900, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377 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
BJE Query on BJE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain V [auth F] SDF format, chain O [auth D] SDF format, chain T [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain V [auth F] MOL2 format, chain O [auth D] MOL2 format, chain T [auth E]	H [auth A] I [auth B] M [auth C] O [auth D] T [auth E] H [auth A], I [auth B], M [auth C], O [auth D], T [auth E], V [auth F]	2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil C₉ H₁₀ N₂ O₅ UUGITDASWNOAGG-XVFCMESISA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain T [auth E] Focus chain V [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F]	J [auth B] K [auth B] P [auth D] Q [auth D] R [auth D] J [auth B], K [auth B], P [auth D], Q [auth D], R [auth D], X [auth F], Y [auth F], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain W [auth F] MOL2 format, chain W [auth F]	W [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain W [auth F] Interactions & Density Focus chain W [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain L [auth C] MOL2 format, chain AA [auth F] MOL2 format, chain L [auth C]	AA [auth F], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain L [auth C] Interactions & Density Focus chain AA [auth F] Focus chain L [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E]	U [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain S [auth E] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain S [auth E]	G [auth A], N [auth C], S [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Focus chain S [auth E] Interactions & Density Focus chain G [auth A] Focus chain N [auth C] Focus chain S [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.169
R-Value Work: 0.135
R-Value Observed: 0.136
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.245	α = 90
b = 93.245	β = 90
c = 152.928	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Prokofev, I.I.

Eistrikh-Geller, P.A.

This entry supersedes: 5OUR

Funding Organization	Location	Grant Number
Other government	Russian Federation	MK-9246.2016.3.

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2020-11-25
Changes: Database references, Derived calculations
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description