[English] 日本語
Yorodumi
- PDB-7q2w: Mutant T91S of uridine phosphorylase from Shewanella oneidensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q2w
TitleMutant T91S of uridine phosphorylase from Shewanella oneidensis
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / uridine phosphorylase / mutant enzyme
Function / homology
Function and homology information


uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
URACIL / Uridine phosphorylase
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.654 Å
AuthorsPolyakov, K. / Safonova, T.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Not funded Russian Federation
CitationJournal: Crystallography Reports / Year: 2021
Title: Role of conformational changes of hexameric bacterial uridine phosphorylases in substrate binding
Authors: Polyakov, K.M. / Mordkovich, N.N. / Safonova, T.N. / Antipov, A.N. / Okorokova, N.A. / Dorovatovskii, P.V. / Veiko, V.P.
History
DepositionOct 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
DDD: Uridine phosphorylase
FFF: Uridine phosphorylase
AAA: Uridine phosphorylase
CCC: Uridine phosphorylase
EEE: Uridine phosphorylase
BBB: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,36316
Polymers160,3956
Non-polymers96910
Water15,115839
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23300 Å2
ΔGint-238 kcal/mol
Surface area42750 Å2
Unit cell
Length a, b, c (Å)91.400, 95.490, 91.410
Angle α, β, γ (deg.)90.000, 120.025, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Uridine phosphorylase


Mass: 26732.455 Da / Num. of mol.: 6 / Mutation: T91S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Strain: MR-1 / Gene: udp, SO_4133 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8E9X9, uridine phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris, pH 6.5, 0.2 M ammonium sulfate, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.964 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.0823
pseudo-merohedral11-L, -K, -H20.4491
pseudo-merohedral11-H-L, -K, L30.1358
pseudo-merohedral11L, K, -H-L40.04
pseudo-merohedral11-H-L, K, H50.2085
pseudo-merohedral11-H, -K, H+L60.0842
ReflectionResolution: 1.65→25 Å / Num. obs: 159146 / % possible obs: 97 % / Redundancy: 5.09 % / CC1/2: 0.99 / Net I/σ(I): 8.8
Reflection shellResolution: 1.65→1.75 Å / Num. unique obs: 23356 / CC1/2: 0.88

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2X

4r2x


Resolution: 1.654→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.714 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.023
RfactorNum. reflection% reflection
Rfree0.2324 7780 4.889 %
Rwork0.1909 151365 -
all0.193 --
obs-159145 98.289 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.455 Å2
Baniso -1Baniso -2Baniso -3
1--18.41 Å2-0 Å2-8.14 Å2
2--32.512 Å20 Å2
3----14.102 Å2
Refinement stepCycle: LAST / Resolution: 1.654→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10898 0 55 839 11792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01311188
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710420
X-RAY DIFFRACTIONr_angle_refined_deg2.3151.63915226
X-RAY DIFFRACTIONr_angle_other_deg1.5371.56724023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.69651463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87621.489517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.799151738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0491577
X-RAY DIFFRACTIONr_chiral_restr0.1160.21547
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212700
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022339
X-RAY DIFFRACTIONr_nbd_refined0.2140.22780
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.211331
X-RAY DIFFRACTIONr_nbtor_refined0.1770.25320
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.25365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2888
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1090.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.230
X-RAY DIFFRACTIONr_nbd_other0.2280.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2120.21
X-RAY DIFFRACTIONr_mcbond_it2.1791.7915879
X-RAY DIFFRACTIONr_mcbond_other2.1781.795878
X-RAY DIFFRACTIONr_mcangle_it2.9162.6867330
X-RAY DIFFRACTIONr_mcangle_other2.9162.6867331
X-RAY DIFFRACTIONr_scbond_it2.1971.935309
X-RAY DIFFRACTIONr_scbond_other2.1941.9285302
X-RAY DIFFRACTIONr_scangle_it2.9252.8427895
X-RAY DIFFRACTIONr_scangle_other2.9232.847884
X-RAY DIFFRACTIONr_lrange_it4.35122.00812880
X-RAY DIFFRACTIONr_lrange_other4.35122.00812881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.654-1.6970.3725080.2939888X-RAY DIFFRACTION87.6782
1.697-1.7430.315290.25610886X-RAY DIFFRACTION97.8988
1.743-1.7940.2985650.24410630X-RAY DIFFRACTION98.4695
1.794-1.8490.2785340.23110178X-RAY DIFFRACTION98.4107
1.849-1.910.2835170.22110127X-RAY DIFFRACTION98.7567
1.91-1.9770.3075050.2389620X-RAY DIFFRACTION98.9736
1.977-2.0510.2875520.2239247X-RAY DIFFRACTION98.9298
2.051-2.1350.2794690.2069081X-RAY DIFFRACTION99.1899
2.135-2.230.254050.2078749X-RAY DIFFRACTION98.9515
2.23-2.3380.2185090.1978209X-RAY DIFFRACTION99.4865
2.338-2.4650.2043770.1887973X-RAY DIFFRACTION99.6539
2.465-2.6140.274340.1967464X-RAY DIFFRACTION99.7348
2.614-2.7940.2293320.1897000X-RAY DIFFRACTION99.3361
2.794-3.0180.2253420.1776602X-RAY DIFFRACTION100.0144
3.018-3.3060.2023080.1786153X-RAY DIFFRACTION99.9227
3.306-3.6950.1642480.1645501X-RAY DIFFRACTION99.9652
3.695-4.2650.1542400.144871X-RAY DIFFRACTION99.9023
4.265-5.220.1611650.1364149X-RAY DIFFRACTION99.9768
5.22-7.3660.1781450.1433261X-RAY DIFFRACTION99.912
7.366-250.125960.1311776X-RAY DIFFRACTION97.9592

+
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://pdbjlvh1.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