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- PDB-3twm: Crystal structure of Arabidopsis thaliana FPG -

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Basic information

Entry
Database: PDB / ID: 3twm
TitleCrystal structure of Arabidopsis thaliana FPG
Components
  • 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3'
  • 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'
  • Formamidopyrimidine-DNA glycosylase 1
KeywordsHYDROLASE/DNA / HELIX TWO TURNS HELIX / ZINC-LESS FINGER / HYDROLASE / DNA DAMAGE / DNA REPAIR / DNA-BINDING / GLYCOSIDASE / LYASE / MULTIFUNCTIONAL ENZYME / DNA containing stable analog of abasic site / Tetrahydro Furan / HYDROLASE-DNA complex
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
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase 1
B: Formamidopyrimidine-DNA glycosylase 1
C: 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3'
D: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'
E: 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3'
F: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)88,7526
Polymers88,7526
Non-polymers00
Water2,576143
1
A: Formamidopyrimidine-DNA glycosylase 1
C: 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3'
D: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)44,3763
Polymers44,3763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-19 kcal/mol
Surface area16140 Å2
MethodPISA
2
B: Formamidopyrimidine-DNA glycosylase 1
E: 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3'
F: 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)44,3763
Polymers44,3763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-18 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.400, 98.570, 181.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Formamidopyrimidine-DNA glycosylase 1


Mass: 34686.711 Da / Num. of mol.: 2
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: DNA chain 5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3'


Mass: 4710.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Purchased from Operon Technology
#3: DNA chain 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3'


Mass: 4979.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Purchased from Operon Technology
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% (v/v) PEG 2000 MME, 100 mM KBr, and 100 mM sodium acetate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2009
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→19.958 Å / Num. all: 21150 / Num. obs: 21150 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rsym value: 0.094 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.955.90.5381.41770529770.53897.6
2.95-3.1360.3072.51724928580.30799
3.13-3.356.20.17941689227220.17999.9
3.35-3.616.50.1315.11645625500.131100
3.61-3.966.60.16.11564423570.1100
3.96-4.436.70.08271435121370.082100
4.43-5.116.60.0767.21269419180.076100
5.11-6.266.30.086.91025516310.0899.8
6.26-8.856.10.0687.3793112960.06899.5
8.85-19.9586.20.0598.643947040.05991.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.12data scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TWL

3twl


Resolution: 2.8→19.958 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 2078 9.8 %RANDOM
Rwork0.225 ---
obs-21101 99.3 %-
Solvent computationBsol: 56.1448 Å2
Displacement parametersBiso max: 144.36 Å2 / Biso mean: 69.2341 Å2 / Biso min: 34.31 Å2
Baniso -1Baniso -2Baniso -3
1-10.087 Å20 Å20 Å2
2--5.55 Å20 Å2
3----15.637 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 1246 0 143 5502
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.295
X-RAY DIFFRACTIONc_mcbond_it1.3771.5
X-RAY DIFFRACTIONc_scbond_it1.9242
X-RAY DIFFRACTIONc_mcangle_it2.3822
X-RAY DIFFRACTIONc_scangle_it3.1292.5
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

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