[English] 日本語
Yorodumi
- PDB-6rca: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rca
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with 2.2'-anhydrouridine at 1.34 A
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / metal ion binding / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.345 Å
AuthorsProkofev, I.I. / Eistrikh-Geller, P.A. / Balaev, V.V. / Gabdoulkhakov, A.G. / Betzel, C. / Lashkov, A.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Other governmentMK-9246.2016.3. Russian Federation
CitationJournal: Crystallography Reports / Year: 2020
Title: X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine
Authors: Eistrikh-Geller, P.A. / Rubinsky, S.V. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Mironov, A.S. / Lashkov, A.A.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionMay 13, 2020ID: 5OUR
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,97427
Polymers162,6546
Non-polymers2,32021
Water35,5801975
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23520 Å2
ΔGint-159 kcal/mol
Surface area47310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.245, 93.245, 152.928
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Uridine phosphorylase


Mass: 27108.994 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

-
Non-polymers , 7 types, 1996 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-BJE / 2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil / Anhydrouridine / 2,2'-ANHYDROURIDINE / CYCLOURIDINE


Mass: 226.186 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H10N2O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1975 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0,2 M MgCl2,6H2O, 15%(w/v) PEG 4000, 0,1 M TRIS -HCl, pH 8.5, 0.2 M 2,2'-anhydrouridine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.886 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.34→44.596 Å / Num. obs: 329624 / % possible obs: 99.7 % / Redundancy: 10.281 % / Biso Wilson estimate: 16.605 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.147 / Χ2: 1.084 / Net I/σ(I): 11.52 / Num. measured all: 3388833
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.34-1.439.7341.2021.951563453492529730.8111.2799
1.43-1.5210.4440.8282.9652426650286502000.9180.87199.8
1.52-1.659.9560.5034.6546493446772467010.9660.5399.8
1.65-1.810.510.3257.145109242978429190.9860.34299.9
1.8-2.0210.4420.18811.3140603638931388840.9950.19899.9
2.02-2.3310.4460.11417.5735847934361343180.9980.1299.9
2.33-2.8510.6040.0823.9530675528962289290.9990.08499.9
2.85-4.0210.4650.05434.0223427422426223870.9990.05799.8
4.02-44.59610.3440.04742.8312736312347123130.9990.04999.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX2.6.1refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6O

4k6o


Resolution: 1.345→44.596 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 19.64
RfactorNum. reflection% reflection
Rfree0.1686 3456 1.05 %
Rwork0.1353 --
obs0.1356 329397 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.42 Å2 / Biso mean: 17.1182 Å2 / Biso min: 2.82 Å2
Refinement stepCycle: final / Resolution: 1.345→44.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11294 0 184 2004 13482
Biso mean--20.6 35.19 -
Num. residues----1508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3448-1.36330.29081350.266127201285597
1.3633-1.38270.25011380.24841298113119100
1.3827-1.40340.25531380.23471300813146100
1.4034-1.42530.28521380.21521308113219100
1.4253-1.44870.26281380.19941302313161100
1.4487-1.47370.2641390.18711309913238100
1.4737-1.50050.19451380.17431306013198100
1.5005-1.52930.19951400.16921309913239100
1.5293-1.56050.24461370.16431297813115100
1.5605-1.59450.20911390.1521304513184100
1.5945-1.63160.18921380.13611312813266100
1.6316-1.67240.18251390.12511300913148100
1.6724-1.71760.15641370.11951305413191100
1.7176-1.76810.14711390.11641304713186100
1.7681-1.82520.14821390.1181310413243100
1.8252-1.89040.15231380.11851297413112100
1.8904-1.96610.16251380.11671309513233100
1.9661-2.05560.14351390.11251305613195100
2.0556-2.1640.15511380.11551310213240100
2.164-2.29960.13741380.11541302013158100
2.2996-2.47710.16191390.12081306413203100
2.4771-2.72640.16521390.12951308013219100
2.7264-3.12080.16171390.12311308113220100
3.1208-3.93150.13881380.11331301713155100
3.9315-44.62060.1311380.1305130161315499

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more