[English] 日本語
Yorodumi
- PDB-4jp5: X-ray structure of uridine phosphorylase from Yersinia pseudotube... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jp5
TitleX-ray structure of uridine phosphorylase from Yersinia pseudotuberculosis in unliganded state at 2.27 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold / uridine / phosphate ion
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / cytoplasm
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 pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsBalaev, V.V. / Lashkov, A.A. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To be Published
Title: X-ray structure of uridine phosphorylase from Yersinia pseudotuberculosis in unliganded state at 2.27 A resolution
Authors: Balaev, V.V. / Lashkov, A.A. / Prokofev, I.I. / Gabdoulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)163,21612
Polymers162,7506
Non-polymers4666
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20640 Å2
ΔGint-125 kcal/mol
Surface area46240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.750, 93.750, 146.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Uridine phosphorylase


Mass: 27124.955 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 16-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: udp, y0444, YP_3263 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8D1I4, uridine phosphorylase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10mM Tris HCl, 0.1M Tris-maleate-NaOH,20% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Wavelength: 0.8266 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012
RadiationMonochromator: Large Offset Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.626
11-H-K, K, -L20.374
ReflectionResolution: 2.27→48.86 Å / Num. all: 66646 / Num. obs: 65380 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.597 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.27-2.450.380.9281.55492013641124621.05291.4
2.45-2.60.6780.612.7846744868686830.676100
2.6-2.80.8220.4223.9344926882088070.47199.9
2.8-30.9140.2836.1236159663566320.314100
3-3.50.9770.1511.015559610653106380.16799.9
3.5-40.9920.0820.2632790599459930.089100
4-60.9970.04930.2745641858785800.05599.9
6-100.9990.03538.6314622281228080.03999.9
10-200.9990.02651.8534626886880.029100
20-300.9990.02457.6229568680.028100
30-48.860.9990.02343.485230210.02870

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxCuBE(ESRF)data collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DPS

3dps


Resolution: 2.27→48.86 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1788 / WRfactor Rwork: 0.1604 / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8699 / SU B: 4.655 / SU ML: 0.114 / SU R Cruickshank DPI: 0.0715 / SU Rfree: 0.0424 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 3197 4.9 %RANDOM
Rwork0.1781 ---
all0.1792 65379 --
obs0.1792 65379 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.9 Å2 / Biso mean: 35.5649 Å2 / Biso min: 4.11 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å20 Å2
2---2.92 Å20 Å2
3---5.84 Å2
Refinement stepCycle: LAST / Resolution: 2.27→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10788 0 29 463 11280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02111024
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.94514950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55251435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05323.523440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1151802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9621573
X-RAY DIFFRACTIONr_chiral_restr0.0590.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218181
X-RAY DIFFRACTIONr_mcbond_it0.191.57129
X-RAY DIFFRACTIONr_mcangle_it0.341211462
X-RAY DIFFRACTIONr_scbond_it0.22333895
X-RAY DIFFRACTIONr_scangle_it0.3814.53486
LS refinement shellResolution: 2.269→2.328 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 190 -
Rwork0.279 3533 -
all-3723 -
obs--75.18 %

+
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