[English] 日本語
Yorodumi
- PDB-1ui0: Crystal Structure Of Uracil-DNA Glycosylase From Thermus Thermoph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ui0
TitleCrystal Structure Of Uracil-DNA Glycosylase From Thermus Thermophilus HB8
ComponentsUracil-DNA Glycosylase
KeywordsHYDROLASE / Base Excision Repair / Uracil-DNA Glycosylase / Iron/Sulfer Cluster / Thermophile / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding
Similarity search - Function
Uracil-DNA glycosylase family 4 / : / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / URACIL / Type-4 uracil-DNA glycosylase / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHoseki, J. / Okamoto, A. / Masui, R. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Family 4 Uracil-DNA Glycosylase from Thermus thermophilus HB8
Authors: Hoseki, J. / Okamoto, A. / Masui, R. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJul 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 28, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.value
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uracil-DNA Glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6705
Polymers22,9981
Non-polymers6724
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.429, 59.512, 80.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Uracil-DNA Glycosylase


Mass: 22997.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: tthung / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7WYV4, UniProt: Q5SKC5*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.24 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2-1.5M ammonium sulfate, 75mM Tris, 25% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
21.3 Mammonium sulfate1drop
325 %glycerol1drop
475 mMTris-HCl1droppH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.98 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 23, 2002
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→48.2 Å / Num. obs: 35830 / % possible obs: 99.9 % / Biso Wilson estimate: 10.1 Å2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 163400 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.133

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Selenomethionyl uracil-DNA glycosylase from Thermus thermophilus HB8

Resolution: 1.5→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 87702.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3543 9.9 %RANDOM
Rwork0.183 ---
obs0.183 35638 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.448 Å2 / ksol: 0.481203 e/Å3
Displacement parametersBiso mean: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2--0.39 Å20 Å2
3---2.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.02 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 29 202 1743
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.931.5
X-RAY DIFFRACTIONc_mcangle_it1.412
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.512.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.209 623 10.8 %
Rwork0.185 5158 -
obs--98.8 %
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18

+
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