[English] 日本語
Yorodumi
- PDB-7p9z: Crystal structure of a trapped Pab-AGOG/double-standed DNA covale... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p9z
TitleCrystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)
Components
  • DNA (5'-D(*AP*GP*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*(PED)*TP*TP*TP*CP*T)-3')
  • N-glycosylase/DNA lyase
KeywordsHYDROLASE / 8-oxoguanine DNA glycosylase / Pyrococcus abyssi / trapped double-stranded DNA intermediate
Function / homology
Function and homology information


oxidized base lesion DNA N-glycosylase activity / 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
N-glycosylase/DNA lyase-like / N-glycosylase/DNA lyase / N-glycosylase/DNA lyase / DNA glycosylase
Similarity search - Domain/homology
DNA / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsCoste, F. / Goffinont, S. / Flament, D. / Castaing, B.
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.
Authors: Franck, C. / Stephane, G. / Julien, C. / Virginie, G. / Martine, G. / Norbert, G. / Fabrice, C. / Didier, F. / Josef, S.M. / Bertrand, C.
History
DepositionJul 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: DNA (5'-D(*TP*TP*TP*(PED)*TP*TP*TP*CP*T)-3')
I: DNA (5'-D(*AP*GP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4464
Polymers33,3283
Non-polymers1181
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-12 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.848, 68.775, 68.424
Angle α, β, γ (deg.)90.000, 90.350, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21A-598-

HOH

-
Components

#1: Protein N-glycosylase/DNA lyase / 8-oxoguanine DNA glycosylase / AGOG / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 27982.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: PYRAB10170, PAB1695 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UZY0, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*TP*TP*TP*(PED)*TP*TP*TP*CP*T)-3')


Mass: 2555.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2789.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MgCl2, Na acetate pH 5.0, MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.33→68.42 Å / Num. obs: 66075 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.2
Reflection shellResolution: 1.33→1.35 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3311 / CC1/2: 0.924

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OY7

7oy7


Resolution: 1.33→45.99 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 3294 4.99 %
Rwork0.174 62748 -
obs0.1746 66042 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.74 Å2 / Biso mean: 29.2071 Å2 / Biso min: 14.54 Å2
Refinement stepCycle: final / Resolution: 1.33→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 354 8 317 2611
Biso mean--21.55 37.36 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.33-1.340.28421510.260525832734100
1.34-1.360.28631310.246626262757100
1.36-1.390.25481140.240326042718100
1.39-1.410.2691240.23226592783100
1.41-1.430.2531480.215726112759100
1.43-1.460.21091570.208225932750100
1.46-1.490.22021580.201226082766100
1.49-1.520.2731350.199326092744100
1.52-1.550.21481230.192126332756100
1.55-1.590.20441290.195726582787100
1.59-1.630.20511470.190225952742100
1.63-1.670.24921350.193726202755100
1.67-1.720.21021260.200126682794100
1.72-1.770.22831210.201226152736100
1.77-1.840.19631130.194526472760100
1.84-1.910.18471610.188926002761100
1.91-20.22351280.187126522780100
2-2.10.18631540.181726252779100
2.1-2.240.19691770.174925622739100
2.24-2.410.16531340.164926522786100
2.41-2.650.17411250.173126362761100
2.65-3.030.17021360.175126582794100
3.03-3.820.16271580.14612633279199
3.82-45.990.17141090.15542401251088
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1261-0.9573-0.80356.0248-3.13346.1046-0.2286-0.14530.28720.43740.2389-0.4813-0.11290.324-0.04440.26430.0289-0.03810.3671-0.04640.240616.195617.840932.8583
26.9471-3.1792-4.09018.51584.95495.17320.11240.15550.67340.2210.0495-0.30320.24490.3219-0.11410.29720.0743-0.02680.58360.05950.36420.816815.469635.4256
31.6478-0.4918-0.37935.90470.72591.49970.0955-0.11990.22790.0012-0.1094-0.0533-0.09020.06930.00750.1058-0.0131-0.0060.13710.00020.13998.025126.75146.0175
41.8374-0.2531-0.2091.14560.28442.50740.0069-0.3148-0.20120.1194-0.05-0.00290.26060.04790.03520.1625-0.02770.00970.17630.04430.14666.41411.990217.867
51.32440.95270.09831.48210.4153.05130.1627-0.25220.12820.0839-0.0903-0.0299-0.15780.2736-0.06880.1513-0.00710.0060.1627-0.04090.20489.68834.047113.0919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 9 )B1 - 9
2X-RAY DIFFRACTION2chain 'I' and (resid 1 through 9 )I1 - 9
3X-RAY DIFFRACTION3chain 'A' and (resid -2 through 36 )A-2 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 159 )A37 - 159
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 239 )A160 - 239

+
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