[English] 日本語
Yorodumi
- PDB-3fwp: X-ray structure of uridine nucleoside phosphorylease from Salmone... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fwp
TitleX-ray structure of uridine nucleoside phosphorylease from Salmonella typhimurium complexed with phosphate and its inhibitor 2,2'-anhydrouridine at 1.86 A resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Cytoplasm / Glycosyltransferase
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / nucleoside catabolic process / 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-arabinofuranosyl)uracil / : / PHOSPHATE ION / Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLashkov, S.A. / Mikhailov, A.M. / Gabdulkhakov, A.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution.
Authors: Lashkov, A.A. / Zhukhlistova, N.E. / Gabdoulkhakov, A.H. / Shtil, A.A. / Efremov, R.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Structure summary / Category: entity / software
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _software.classification / _software.name
Revision 1.3Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

-
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)164,09515
Polymers163,0156
Non-polymers1,0819
Water18,2851015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22230 Å2
ΔGint-118 kcal/mol
Surface area43840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.790, 124.070, 134.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Uridine phosphorylase / / UrdPase / UPase


Mass: 27169.092 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: STM3968, STMD1.21, udp / Plasmid: PBLUESCRIPT IISK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 / References: UniProt: P0A1F6, uridine phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ANU / 2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil / Anhydrouridine / 2,2'-ANHYDROURIDINE / CYCLOURIDINE


Mass: 226.186 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H10N2O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1015 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG400, NaN3, GLYCEROL, PEG3350. K2HPO4, ANU, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.85 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 21, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.86→88 Å / Num. all: 124633 / Num. obs: 110180 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.094
Reflection shellResolution: 1.86→1.87 Å / Mean I/σ(I) obs: 2.49 / Num. unique all: 1963 / Rsym value: 0.506 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DPS

3dps


Resolution: 1.86→27.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.428 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20617 5509 5 %RANDOM
Rwork0.17615 ---
obs0.17765 104669 88.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.376 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.86→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10965 0 66 1015 12046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211211
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.96415209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59651464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06423.364437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.966151897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7241585
X-RAY DIFFRACTIONr_chiral_restr0.0690.21791
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028280
X-RAY DIFFRACTIONr_nbd_refined0.190.26120
X-RAY DIFFRACTIONr_nbtor_refined0.2940.27778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.21229
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.231
X-RAY DIFFRACTIONr_mcbond_it0.4361.57218
X-RAY DIFFRACTIONr_mcangle_it0.819211607
X-RAY DIFFRACTIONr_scbond_it1.07234020
X-RAY DIFFRACTIONr_scangle_it1.9224.53591
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 419 -
Rwork0.248 7966 -
obs--92.61 %

+
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