[English] 日本語
Yorodumi
- PDB-7z5r: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z5r
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH012035
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / OGG1 / glycosylase / inhibitor
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / negative regulation of double-strand break repair via single-strand annealing / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / DNA N-glycosylase activity ...Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / negative regulation of double-strand break repair via single-strand annealing / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / DNA N-glycosylase activity / oxidized purine nucleobase lesion DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to light stimulus / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to cadmium ion / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / response to radiation / nuclear matrix / response to estradiol / microtubule binding / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / response to xenobiotic stimulus / DNA repair / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus
Similarity search - Function
8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
Chem-IGQ / NICKEL (II) ION / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, J.R. / Scaletti, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: To Be Published
Title: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH012035
Authors: Davies, J.R. / Scaletti, E. / Stenmark, P.
History
DepositionMar 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: N-glycosylase/DNA lyase
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3147
Polymers107,4503
Non-polymers8644
Water2,288127
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1443
Polymers35,8171
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0852
Polymers35,8171
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0852
Polymers35,8171
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.459, 81.533, 170.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein N-glycosylase/DNA lyase


Mass: 35816.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ogg1 / Production host: Escherichia coli (E. coli)
References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-IGQ / (7~{R})-~{N}-(4,5,6,7-tetrahydro-1,2-benzoxazol-3-yl)bicyclo[4.2.0]octa-1,3,5-triene-7-carboxamide


Mass: 268.310 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Alcohols, 0.1M Buffer System 1 pH 6.5, 30.0 % v/v GOL_P4K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→170.2 Å / Num. obs: 40059 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.997 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 4457 / CC1/2: 0.586

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3Y

6g3y


Resolution: 2.5→85.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.937 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29377 1960 4.9 %RANDOM
Rwork0.23667 ---
obs0.23946 37989 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.249 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2---1.63 Å20 Å2
3---0.67 Å2
Refinement stepCycle: 1 / Resolution: 2.5→85.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7067 0 61 127 7255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197334
X-RAY DIFFRACTIONr_bond_other_d0.0020.026701
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.94110024
X-RAY DIFFRACTIONr_angle_other_deg0.925315254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77222.555317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.818151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7841553
X-RAY DIFFRACTIONr_chiral_restr0.0640.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021839
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6527.2013673
X-RAY DIFFRACTIONr_mcbond_other3.6537.2013672
X-RAY DIFFRACTIONr_mcangle_it5.87810.7774572
X-RAY DIFFRACTIONr_mcangle_other5.87810.7784573
X-RAY DIFFRACTIONr_scbond_it3.1717.1683661
X-RAY DIFFRACTIONr_scbond_other3.177.1683662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.24810.7055447
X-RAY DIFFRACTIONr_long_range_B_refined8.40756.3878070
X-RAY DIFFRACTIONr_long_range_B_other8.40656.4038062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 166 -
Rwork0.376 2745 -
obs--99.66 %

+
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