6Z9Z

Atomic resolution X-ray structure of the Uridine phosphorylase from Vibrio cholerae on crystals grown under microgravity

PDB DOI: https://doi.org/10.2210/pdb6Z9Z/pdb

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

Deposited: 2020-06-04 Released: 2021-06-30
Deposition Author(s): Eistrikh-Heller, P.A., Rubinsky, S.V., Samygina, V.R., Gabdulkhakov, A.G., Lashkov, A.A.
Funding Organization(s): Russian Foundation for Basic Research, Ministry of Education and Science of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free: 0.142
R-Value Work: 0.126
R-Value Observed: 0.126

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystallization in Microgravity and the Atomic-Resolution Structure of Uridine Phosphorylase from Vibrio cholerae

Eistrikh-Heller, P.A., Rubinsky, S.V., Samygina, V.R., Gabdulkhakov, A.G., Kovalchuk, M.V., Mironov, A.S., Lashkov, A.A.

(2021) Crystallogr Rep 66: 777-785

DOI: https://doi.org/10.1134/S1063774521050059

Macromolecule Content

Total Structure Weight: 164.37 kDa
Atom Count: 14,294
Modelled Residue Count: 1,499
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, BC353_05040, C9J66_05900, D2927_05805, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032... udp, udp_1, BC353_05040, C9J66_05900, D2927_05805, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377, FLM02_10845, FXF03_16695 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain W [auth C]	CA [auth D], W [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain W [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	EA [auth E], G [auth A], L [auth B], S [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain EA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain KA [auth F] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain FA [auth E] SDF format, chain N [auth B] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain FA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain Y [auth D]	DA [auth E] FA [auth E] H [auth A] I [auth A] KA [auth F] DA [auth E], FA [auth E], H [auth A], I [auth A], KA [auth F], LA [auth F], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain FA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain FA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain Y [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain IA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain IA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain IA [auth E]	BA [auth D], IA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain IA [auth E] Interactions & Density Focus chain BA [auth D] Focus chain IA [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] SDF format, chain T [auth C] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C]	AA [auth D] GA [auth E] HA [auth E] J [auth A] JA [auth E] AA [auth D], GA [auth E], HA [auth E], J [auth A], JA [auth E], K [auth A], P [auth B], T [auth C], U [auth C], V [auth C], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free: 0.142
R-Value Work: 0.126
R-Value Observed: 0.126
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.186	α = 90
b = 97.061	β = 119.965
c = 93.227	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

Eistrikh-Heller, P.A.

Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	19-29-12054
Ministry of Education and Science of the Russian Federation	Russian Federation	0026-2019-0002

Revision History (Full details and data files)

Version 1.0: 2021-06-30
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-04-10
Changes: Database references