[English] 日本語
Yorodumi
- PDB-9o02: Crystal structure of AfOgg1-K122S mutant bound to 8-OG DNA duplex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9o02
TitleCrystal structure of AfOgg1-K122S mutant bound to 8-OG DNA duplex in an intermediate state
Components
  • 8-oxoguanine DNA glycosylase/AP lyase
  • DNA (5'-D(*TP*AP*GP*AP*GP*TP*CP*(8OG)P*AP*CP*CP*TP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*TP*A)-3')
KeywordsHYDROLASE / LYASE/DNA / DNA-glycosylase / AP-lyase / LYASE-DNA complex
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair
Similarity search - Function
8-oxoguanine DNA glycosylase/AP lyase Ogg / 8-oxoguanine DNA glycosylase / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
MOLYBDATE ION / DNA / DNA (> 10) / 8-oxoguanine DNA glycosylase/AP lyase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuffman, J.L. / Syed, A. / Tang, H.Y.H. / Arvai, A.S. / Mol, C.D. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
CitationJournal: To Be Published
Title: Crystal structure of AfOgg1-K122S mutant bound to 8-OG DNA duplex in an intermediate state
Authors: Huffman, J.L. / Syed, A. / Tang, H.Y.H. / Arvai, A.S. / Mol, C.D. / Tainer, J.A.
History
DepositionApr 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 8-oxoguanine DNA glycosylase/AP lyase
B: DNA (5'-D(*TP*AP*GP*AP*GP*TP*CP*(8OG)P*AP*CP*CP*TP*GP*CP*A)-3')
C: DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4814
Polymers32,3213
Non-polymers1601
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-15 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.540, 52.833, 52.339
Angle α, β, γ (deg.)90.00, 96.06, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 8-oxoguanine DNA glycosylase/AP lyase


Mass: 23125.824 Da / Num. of mol.: 1 / Mutation: K122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: ogg, AF_0371 / Production host: Escherichia coli (E. coli)
References: UniProt: O29876, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*TP*AP*GP*AP*GP*TP*CP*(8OG)P*AP*CP*CP*TP*GP*CP*A)-3')


Mass: 4609.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*AP*GP*GP*TP*CP*GP*AP*CP*TP*CP*TP*A)-3')


Mass: 4584.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG4000, 100 mM MES, pH 6.5, 5% potassium permanganate (saturated)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9648 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9648 Å / Relative weight: 1
ReflectionResolution: 2.5→52.05 Å / Num. obs: 9608 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 468 / CC1/2: 0.436

-
Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
autoPROCdata processing
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→52.05 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 503 5.28 %
Rwork0.2199 --
obs0.2228 9525 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→52.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 610 5 3 2044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.64
X-RAY DIFFRACTIONf_dihedral_angle_d24.385824
X-RAY DIFFRACTIONf_chiral_restr0.037353
X-RAY DIFFRACTIONf_plane_restr0.004279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.38951120.35882211X-RAY DIFFRACTION98
2.75-3.150.34311380.29232225X-RAY DIFFRACTION99
3.15-3.970.28361290.21892257X-RAY DIFFRACTION99
3.97-52.050.2371240.1842329X-RAY DIFFRACTION100

+
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