[English] 日本語
Yorodumi
- PDB-7ou3: Crystal structure of Tga-AGOG, an 8-oxoguanine DNA glycosylase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ou3
TitleCrystal structure of Tga-AGOG, an 8-oxoguanine DNA glycosylase from Thermococcus gammatolerans
ComponentsN-glycosylase/DNA lyase
KeywordsHYDROLASE / 8-oxoguanine DNA glycosylase / archaea / Thermococcus gammatolerans
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
N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesThermococcus gammatolerans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsCoste, F. / Confalonieri, F. / 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
DepositionJun 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,2996
Polymers62,0442
Non-polymers2554
Water5,747319
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0572
Polymers31,0221
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2414
Polymers31,0221
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.429, 62.452, 139.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 31021.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) (archaea)
Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: TGAM_1653 / Production host: Escherichia coli (E. coli)
References: UniProt: C5A7E3, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Hepes, NaCl, PEG 1500, glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.49→69.94 Å / Num. obs: 88713 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.6
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4393 / CC1/2: 0.832 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xqo

1xqo


Resolution: 1.49→46.15 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1918 4390 4.95 %
Rwork0.1722 84309 -
obs0.1732 88699 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.09 Å2
Refinement stepCycle: LAST / Resolution: 1.49→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 14 319 4185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554011
X-RAY DIFFRACTIONf_angle_d0.7665457
X-RAY DIFFRACTIONf_chiral_restr0.0698607
X-RAY DIFFRACTIONf_plane_restr0.0073705
X-RAY DIFFRACTIONf_dihedral_angle_d11.61821487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.25771350.23512753X-RAY DIFFRACTION99.97
1.51-1.520.23841430.22322782X-RAY DIFFRACTION99.9
1.52-1.540.26681320.21072805X-RAY DIFFRACTION100
1.54-1.560.21481420.20912773X-RAY DIFFRACTION99.9
1.56-1.580.23521760.20242747X-RAY DIFFRACTION99.97
1.58-1.60.22951370.19552772X-RAY DIFFRACTION100
1.6-1.630.20871330.21272803X-RAY DIFFRACTION100
1.63-1.650.21171300.20762796X-RAY DIFFRACTION99.97
1.65-1.680.22981580.20752780X-RAY DIFFRACTION100
1.68-1.70.22471440.20242779X-RAY DIFFRACTION99.97
1.7-1.730.24011460.18772776X-RAY DIFFRACTION99.97
1.73-1.770.19271430.17222792X-RAY DIFFRACTION99.93
1.77-1.80.1851680.17382768X-RAY DIFFRACTION99.97
1.8-1.840.17851630.1692775X-RAY DIFFRACTION100
1.84-1.880.20351470.16872776X-RAY DIFFRACTION99.93
1.88-1.920.22811340.16982832X-RAY DIFFRACTION99.97
1.92-1.970.19461380.17762790X-RAY DIFFRACTION100
1.97-2.020.20581540.19062785X-RAY DIFFRACTION100
2.02-2.080.16831510.1652802X-RAY DIFFRACTION99.97
2.08-2.150.19561500.17082793X-RAY DIFFRACTION100
2.15-2.220.19811390.16622820X-RAY DIFFRACTION99.9
2.22-2.310.18351220.16722852X-RAY DIFFRACTION100
2.31-2.420.1871360.16572818X-RAY DIFFRACTION99.86
2.42-2.550.20321700.16772791X-RAY DIFFRACTION100
2.55-2.710.17721580.16822836X-RAY DIFFRACTION100
2.71-2.910.18381410.16532841X-RAY DIFFRACTION99.97
2.92-3.210.17381660.16912827X-RAY DIFFRACTION99.97
3.21-3.670.15091450.16292902X-RAY DIFFRACTION99.87
3.67-4.630.17721390.14772900X-RAY DIFFRACTION99.87
4.63-46.150.22371500.18643043X-RAY DIFFRACTION99.5
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)
13.39148127705-2.57989724339-2.320127196472.853322015071.591082912691.85215964019-0.175888602456-0.310680405975-0.3170548793970.1369453115310.108295261266-0.08953517026840.2573658072270.326329732830.06134641974890.1988473249240.0442048030733-0.006054829532920.2233777764780.01418108064410.26067402914294.3791562321180.044834276281.987859503
21.436439929090.457719220298-0.3544963064721.9921581137-0.09153492873081.978237875630.0696747471130.01457593417380.031272523106-0.0183850553127-0.03459554814060.0540932553403-0.117192043196-0.0531796861349-0.03680956082910.1225760878050.008993621848150.01843756573170.1578898128160.001208981349250.14738155237381.2148935857196.797885955279.115068678
35.99949151243-2.33659936368-2.472433690813.78271004581.792424344431.995901447550.257162533826-0.1374400117510.310068321584-0.405271404635-0.020975773534-0.772632082493-0.1970661142010.336719383603-0.2114932710970.2859381071080.02473101321690.06720414160220.2202370031720.01207185170350.37873284332397.7847161091180.076081711275.898951641
41.312169419741.245765732620.4516438721462.709074525240.1722696152754.03667313977-0.378705055726-0.09744996037910.05702949073750.0204883403168-0.0209348624151-0.628598914297-0.4799858128140.575519658350.2748386109010.273156099511-0.0951718267555-0.03212899473630.2933579043210.07217665441120.2776473954279.0507644294189.392812959325.138213558
50.800935715117-0.0292424540409-0.06022668174632.29156755191-0.2511145122051.6696990847-0.02722210190820.0143131778379-0.02295971330010.01774572506720.02590923760130.08915482646910.049400750477-0.0621735913576-0.0002326710552120.117369750873-0.001746440856970.001196053207760.121715736698-0.0004961503471430.12093895166460.5582009513195.04251805305.268368778
62.484018740210.1315629891021.075615518833.02474765772-0.4783641146361.76713650017-0.4569374587740.3619636950170.188109883944-0.4184105811480.205439035154-0.896839450852-0.7921960980860.8208169175820.1321363467940.449643733384-0.2238213137660.04336683221960.4083502022470.03605357243560.38509750872479.170630808189.884676663317.451617202
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 54 )AA11 - 541 - 44
22chain 'A' and (resid 55 through 180 )AA55 - 18045 - 170
33chain 'A' and (resid 181 through 263 )AA181 - 263171 - 248
44chain 'B' and (resid 14 through 39 )BB14 - 391 - 26
55chain 'B' and (resid 40 through 180 )BB40 - 18027 - 167
66chain 'B' and (resid 181 through 263 )BB181 - 263168 - 241

+
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://pdbjlvh1.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