[English] 日本語
Yorodumi
- PDB-5c80: X-ray structure uridine phosphorylase from Vibrio cholerae in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c80
TitleX-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution
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
DI(HYDROXYETHYL)ETHER / URIDINE / Uridine phosphorylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.243 Å
AuthorsProkofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR14-04-00952a Russian Federation
CitationJournal: Crystallography Reports / Year: 2016
Title: 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
Authors: Prokofev, I.I. / Lashkov, A.A. / Gabdoulkhakov, A.G. / Balaev, V.V. / Seregina, T.A. / Mironov, A.S. / Betzel, C. / Mikhailov, A.M.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 10, 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)166,07235
Polymers162,6546
Non-polymers3,41829
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29600 Å2
ΔGint-142 kcal/mol
Surface area44140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.255, 73.110, 83.137
Angle α, β, γ (deg.)71.810, 77.190, 85.690
Int Tables number1
Space group name H-MP1

-
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, DN30_1909, VC39_02535, VC78_02550, VS27_10630, WG08_05660
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K4U1, uridine phosphorylase

-
Non-polymers , 7 types, 851 molecules

#2: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97989 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 2.243→77.231 Å / Num. all: 58293 / Num. obs: 58293 / % possible obs: 91.1 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.055 / Rrim(I) all: 0.077 / Net I/av σ(I): 11.229 / Net I/σ(I): 9.6 / Num. measured all: 101646
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.243-2.361.70.3332.31327178100.3330.3332.383.2
2.36-2.511.80.2183.41479881930.2180.2183.693.2
2.51-2.681.70.1455.11380079130.1450.1454.895.1
2.68-2.91.70.0977.51239673530.0970.0976.794.9
2.9-3.171.80.0710.41234168090.070.079.195.4
3.17-3.551.70.0514.31039659980.050.0512.493.2
3.55-4.11.70.03519.2827147850.0350.03517.184.4
4.1-5.021.80.0320.3723841100.030.032186.3
5.02-7.091.70.03120.1594034550.0310.03120.792.8
7.09-45.4271.70.02619319518670.0260.02626.492.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.03 Å45.43 Å
Translation8.03 Å45.43 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LWZ

4lwz


Resolution: 2.243→45.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2136 / WRfactor Rwork: 0.1515 / FOM work R set: 0.8352 / SU B: 7.17 / SU ML: 0.174 / SU R Cruickshank DPI: 0.5856 / SU Rfree: 0.2644 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.586 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2849 4.9 %RANDOM
Rwork0.1683 ---
obs0.1716 55318 90.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.62 Å2 / Biso mean: 30.999 Å2 / Biso min: 3.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.04 Å20.08 Å2
2---0.17 Å20.01 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.243→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11263 0 167 822 12252
Biso mean--29.06 37.85 -
Num. residues----1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911757
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.97715933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20451514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20523.747459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.511151935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1461580
X-RAY DIFFRACTIONr_chiral_restr0.1180.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218628
X-RAY DIFFRACTIONr_mcbond_it1.5462.9416050
X-RAY DIFFRACTIONr_mcangle_it2.5394.4017538
X-RAY DIFFRACTIONr_scbond_it1.8723.1375707
LS refinement shellResolution: 2.243→2.301 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 173 -
Rwork0.278 3297 -
all-3470 -
obs--72.91 %

+
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