[English] 日本語
Yorodumi
- PDB-4of4: X-ray structure of unliganded uridine phosphorylase from Yersinia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4of4
TitleX-ray structure of unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Rossmann Fold / pyrimidine base / 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
DI(HYDROXYETHYL)ETHER / Uridine phosphorylase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsBalaev, V.V. / Lashkov, A.A. / Gabdulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To be Published
Title: X-ray structure of unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 A resolution
Authors: Balaev, V.V. / Lashkov, A.A. / Gabdulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Experimental preparation
Revision 1.2Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5657
Polymers54,2502
Non-polymers3155
Water7,819434
1
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules

A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules

A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,69621
Polymers162,7506
Non-polymers94615
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 area23740 Å2
ΔGint-118 kcal/mol
Surface area48620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.949, 150.949, 46.231
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Uridine phosphorylase


Mass: 27124.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: udp / Production host: Escherichia coli (E. coli) / Strain (production host): AM201 / References: UniProt: Q7AZX0, uridine phosphorylase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 1.87 Å3/Da / Density % sol: 34.17 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.8
Details: 1M TRIS, 5% W/V PGA-LM, 20% W/V PEG 2000 MME, pH 7.8, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→75.475 Å / Num. all: 76922 / Num. obs: 76922 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.059 / Net I/σ(I): 14.7
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
1.4-1.484.80.6261.253029110960.3190.6262.699
1.48-1.574.80.4031.950752106650.2060.4034.1100
1.57-1.684.90.24934930699870.1250.2496.4100
1.68-1.814.80.1624.54534193550.0820.1629.4100
1.81-1.9850.0967.34248785470.0480.09614.7100
1.98-2.2250.06110.83889277830.0310.06121.3100
2.22-2.5650.04812.93436468320.0240.04826.1100
2.56-3.135.10.04113.52947757580.020.04130.999.9
3.13-4.435.10.0413.32288444710.020.0436.9100
4.43-43.5865.10.04710.91233424280.0230.04737.8100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.59 Å
Translation2.5 Å43.59 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I2V

4i2v


Resolution: 1.4→75.47 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1865 / WRfactor Rwork: 0.1555 / FOM work R set: 0.9024 / SU B: 2.263 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0794 / SU Rfree: 0.0645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 3859 5 %RANDOM
Rwork0.1524 ---
all0.1541 76922 --
obs0.1541 76922 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.98 Å2 / Biso mean: 18.103 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→75.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 20 434 4224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224081
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9465576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65523.86171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91515690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9221527
X-RAY DIFFRACTIONr_chiral_restr0.0760.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213101
X-RAY DIFFRACTIONr_mcbond_it0.6331.52605
X-RAY DIFFRACTIONr_mcangle_it1.10124237
X-RAY DIFFRACTIONr_scbond_it1.73831476
X-RAY DIFFRACTIONr_scangle_it2.7194.51315
X-RAY DIFFRACTIONr_rigid_bond_restr0.7434081
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 277 -
Rwork0.254 5318 -
all-5595 -
obs--98.69 %

+
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