[English] 日本語
Yorodumi
- PDB-3twl: Crystal structure of Arabidopsis thaliana FPG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3twl
TitleCrystal structure of Arabidopsis thaliana FPG
ComponentsFormamidopyrimidine-DNA glycosylase 1
KeywordsHYDROLASE / HELIX TWO TURNS HELIX / ZINC-LESS FINGER / DNA DAMAGE / DNA REPAIR / DNA-BINDING / GLYCOSIDASE / LYASE / MULTIFUNCTIONAL ENZYME
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / response to oxidative stress / damaged DNA binding / DNA repair / zinc ion binding / nucleus
Similarity search - Function
: / Formamidopyrimidine-DNA glycosylase-like, C-terminal domain / Formamidopyrimidine-DNA glycosylase / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain ...: / Formamidopyrimidine-DNA glycosylase-like, C-terminal domain / Formamidopyrimidine-DNA glycosylase / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Formamidopyrimidine-DNA glycosylase / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsDuclos, S. / Aller, P. / Wallace, S.S. / Doublie, S.
CitationJournal: Dna Repair / Year: 2012
Title: Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine.
Authors: Duclos, S. / Aller, P. / Jaruga, P. / Dizdaroglu, M. / Wallace, S.S. / Doublie, S.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7792
Polymers34,6871
Non-polymers921
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.688, 62.448, 97.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Formamidopyrimidine-DNA glycosylase 1


Mass: 34686.711 Da / Num. of mol.: 1 / Fragment: UNP residues 1-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: fpg1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: Q9SBB4, UniProt: O80358*PLUS, DNA-formamidopyrimidine glycosylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% 15/4EO/OH, 150 mM (NH4)2SO4, 50 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 9, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 58601 / % possible obs: 94.7 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.079 / Χ2: 1.03 / Net I/σ(I): 18.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.764.90.44528021.134182.7
1.76-1.837.30.38631501.106191.8
1.83-1.918.80.31131901.146194
1.91-2.029.10.2232491.134194.7
2.02-2.149.10.1632491.143195.3
2.14-2.319.10.12333101.123196.1
2.31-2.549.10.10133411.066196.8
2.54-2.99.10.08533750.995197.6
2.9-3.6690.0734690.831198.3
3.66-208.60.06436440.732199.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.68 Å
Translation2.5 Å19.68 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TWK

3twk


Resolution: 1.7→20 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8557 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 5777 8.8 %RANDOM
Rwork0.2097 ---
obs-58601 89.5 %-
Solvent computationBsol: 57.0818 Å2
Displacement parametersBiso max: 57.15 Å2 / Biso mean: 27.9052 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.226 Å20 Å20 Å2
2--5.606 Å20 Å2
3----6.832 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 6 207 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.322
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_scbond_it2.0292
X-RAY DIFFRACTIONc_mcangle_it1.8492
X-RAY DIFFRACTIONc_scangle_it3.0222.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.710.408560.4218648704
1.71-1.720.5199750.4513691766
1.72-1.740.5475910.4108763854
1.74-1.750.40781120.4122860972
1.75-1.760.47221040.3623792896
1.76-1.770.4265670.37929531020
1.77-1.790.32931160.3559071023
1.79-1.80.3823890.354510111100
1.8-1.820.30581210.33169501071
1.82-1.830.25331020.311810531155
1.83-1.850.3486940.30929361030
1.85-1.860.33141070.30449771084
1.86-1.880.32641330.289110231156
1.88-1.90.2892910.257310441135
1.9-1.910.26131220.237310181140
1.91-1.930.25021270.227610361163
1.93-1.950.23991260.251310861212
1.95-1.970.27011190.242810341153
1.97-1.990.28441060.228310831189
1.99-2.020.25131110.212610781189
2.02-2.040.2527930.203710521145
2.04-2.060.23111230.216511151238
2.06-2.090.21791250.212610771202
2.09-2.110.25191480.21810771225
2.11-2.140.24251220.214811021224
2.14-2.170.25611260.209711161242
2.17-2.20.217960.215211031199
2.2-2.240.25381310.20611171248
2.24-2.270.22761160.183710961212
2.27-2.310.21371150.194711611276
2.31-2.350.19161260.179810731199
2.35-2.390.21941050.202211541259
2.39-2.440.20811280.192111281256
2.44-2.490.25051240.202611021226
2.49-2.540.21781370.21611421279
2.54-2.60.25411430.209611151258
2.6-2.660.231080.204411141222
2.66-2.740.2491400.228411561296
2.74-2.820.22561150.206711531268
2.82-2.910.21521240.210811151239
2.91-3.010.21361480.21811191267
3.01-3.130.2041170.223111841301
3.13-3.270.2035950.213211501245
3.27-3.450.21591300.201511771307
3.45-3.660.1898980.195112071305
3.66-3.940.1611200.172911821302
3.94-4.340.20721460.169811431289
4.34-4.970.1551470.168111521299
4.97-6.260.17961380.206811641302
6.26-200.1991240.203411351259
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5hetero_cpds.parhetero_cpds.top

+
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