[English] 日本語
Yorodumi
- PDB-4i2v: X-ray structure of the unliganded uridine phosphorylase from Yers... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i2v
TitleX-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 2.12A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold / Pyrimidine metabolism
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / 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
Uridine phosphorylase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.121 Å
AuthorsLashkov, A.A. / Balaev, V.V. / Prokofev, I.I. / Betzel, C. / Gabdoulkhakov, A.G. / Mikhailov, A.M.
CitationJournal: To be Published
Title: X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 2.12A resolution
Authors: Lashkov, A.A. / Balaev, V.V. / Prokofev, I.I. / Betzel, C. / Gabdoulkhakov, A.G. / Mikhailov, A.M.
History
DepositionNov 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

-
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


Theoretical massNumber of molelcules
Total (without water)162,7506
Polymers162,7506
Non-polymers00
Water1,29772
1
A: Uridine phosphorylase
B: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)162,7506
Polymers162,7506
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19050 Å2
ΔGint-127 kcal/mol
Surface area47270 Å2
MethodPISA
2
C: Uridine phosphorylase
D: Uridine phosphorylase

C: Uridine phosphorylase
D: Uridine phosphorylase

C: Uridine phosphorylase
D: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)162,7506
Polymers162,7506
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area19150 Å2
ΔGint-131 kcal/mol
Surface area47380 Å2
MethodPISA
3
E: Uridine phosphorylase
F: Uridine phosphorylase

E: Uridine phosphorylase
F: Uridine phosphorylase

E: Uridine phosphorylase
F: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)162,7506
Polymers162,7506
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area19440 Å2
ΔGint-120 kcal/mol
Surface area46930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.680, 156.680, 48.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

-
Components

#1: Protein
Uridine phosphorylase


Mass: 27124.955 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: udp / Production host: Escherichia coli (E. coli) / References: UniProt: Q7AZX0, uridine phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium acetate, 0.1M MES, 10%(w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 13, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.46
ReflectionResolution: 2.12→29.625 Å / Num. obs: 73717 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.12-2.25194
2.25-2.4198.3
2.4-2.59198.2
2.59-2.84198.8
2.84-3.17199
3.17-3.65198.7
3.65-4.46198.2
4.46-6.23198.9
6.23-29.6197.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OXF

2oxf


Resolution: 2.121→29.61 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8289 / σ(F): 2.02 / Phase error: 25.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 3751 5.1 %RANDOM
Rwork0.2003 ---
all0.2041 75394 --
obs0.2032 73600 97.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.03 Å2 / Biso mean: 33.1629 Å2 / Biso min: 11.38 Å2
Refinement stepCycle: LAST / Resolution: 2.121→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 0 0 72 11322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911448
X-RAY DIFFRACTIONf_angle_d1.41615540
X-RAY DIFFRACTIONf_chiral_restr0.11842
X-RAY DIFFRACTIONf_plane_restr0.0072010
X-RAY DIFFRACTIONf_dihedral_angle_d18.0434098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1214-2.15790.29751630.27063091325483
2.1579-2.19720.28141890.27493584377394
2.1972-2.23940.32121840.28763497368193
2.2394-2.28510.48661820.44083461364392
2.2851-2.33470.50271820.46713467364992
2.3347-2.3890.41191820.34553442362492
2.389-2.44870.28781880.23763576376494
2.4487-2.51490.26081840.22773497368194
2.5149-2.58890.26611840.22083506369094
2.5889-2.67240.26771890.22123583377294
2.6724-2.76780.23511840.21133503368794
2.7678-2.87850.24341880.21173575376394
2.8785-3.00930.27921850.20343516370194
3.0093-3.16780.24431850.19163507369293
3.1678-3.3660.22721840.18283499368394
3.366-3.62530.24181860.17483536372293
3.6253-3.98920.2121850.16483517370293
3.9892-4.56430.17471850.14783503368894
4.5643-5.74210.20751850.15693524370993
5.7421-27.79250.19071860.16983519370593

+
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