[English] 日本語
Yorodumi
- PDB-1akz: HUMAN URACIL-DNA GLYCOSYLASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1akz
TitleHUMAN URACIL-DNA GLYCOSYLASE
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsGLYCOSIDASE / GLYCOSYLASE / DNA REPAIR / URACIL REMOVAL FROM DNA / ALPHA/ BETA PROTEIN
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / 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
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.57 Å
AuthorsTainer, J.A. / Mol, C.D.
CitationJournal: Embo J. / Year: 1998
Title: Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
Authors: Parikh, S.S. / Mol, C.D. / Slupphaug, G. / Bharati, S. / Krokan, H.E. / Tainer, J.A.
History
DepositionMay 27, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,5441
Polymers25,5441
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.760, 55.270, 84.970
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 / UDG / UNG


Mass: 25544.137 Da / Num. of mol.: 1 / Mutation: P82M, V83E, G84F
Source method: isolated from a genetically manipulated source
Details: STRUCTURE IS THAT OF RECOMBINANT HUMAN URACIL-DNA GLYCOSYLASE IN WHICH THE 84 N-TERMINAL AMINO ACIDS CODED FOR BY THE UNG GENE HAVE BEEN REPLACED BY THREE RESIDUES FROM THE EXPRESSION VECTOR
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P13051, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.25 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.9
Details: 100 MM IMIDAZOLE/MALEATE, PH 7.9, 1%-4% SATURATED NACL, 1%-4% SATURATED AMMONIUM SULFATE, 16%-20% PEG 4000, MIXED WITH EQUAL VOLUMES 30 MG/ML PROTEIN.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Mol, C.D., (1995) Cell. 80, 869.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
216-20 %PEG40001reservoir
3100 mMimidazole/malate1reservoirpH7.9
41-4 %sat1reservoirNaCl
51-4 %satammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorDate: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 30433 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.9
Reflection shellResolution: 1.57→1.61 Å / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 11 / % possible all: 93.4
Reflection
*PLUS
Num. obs: 30415 / Num. measured all: 121341
Reflection shell
*PLUS
% possible obs: 93.3 % / Rmerge(I) obs: 0.103

-
Processing

Software
NameVersionClassification
PHASESphasing
SQUASHphasing
XTALVIEWrefinement
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.57→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: AN OVERALL BULK SOLVENT CORRECTION WAS APPLIED TO THE DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3048 9.49 %RANDOM
Rwork0.189 ---
obs0.189 30381 94.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9022 Å20 Å20 Å2
2--0.7885 Å20 Å2
3----5.6908 Å2
Refinement stepCycle: LAST / Resolution: 1.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 0 185 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.154
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.949
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.9581.5
X-RAY DIFFRACTIONx_mcangle_it1.6492
X-RAY DIFFRACTIONx_scbond_it1.7462
X-RAY DIFFRACTIONx_scangle_it2.8122.5
LS refinement shellResolution: 1.57→1.64 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.286 390 9.85 %
Rwork0.318 3319 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 29891 / Rfactor obs: 0.187 / Rfactor Rfree: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.96
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.949
LS refinement shell
*PLUS
Rfactor obs: 0.318

+
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