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- PDB-3twk: Crystal structure of arabidopsis thaliana FPG -

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Basic information

Entry
Database: PDB / ID: 3twk
TitleCrystal structure of arabidopsis thaliana FPG
ComponentsFormamidopyrimidine-DNA glycosylase 1DNA-formamidopyrimidine glycosylase
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 / oxidized purine nucleobase lesion 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 / SYNCHROTRON / MAD / Resolution: 2.3 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9304
Polymers66,7462
Non-polymers1842
Water4,882271
1
A: Formamidopyrimidine-DNA glycosylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5573
Polymers33,3731
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Formamidopyrimidine-DNA glycosylase 1


Theoretical massNumber of molelcules
Total (without water)33,3731
Polymers33,3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-21 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.054, 93.054, 157.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Formamidopyrimidine-DNA glycosylase 1 / DNA-formamidopyrimidine glycosylase


Mass: 33372.824 Da / Num. of mol.: 2 / Fragment: UNP residues 1-281
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% (w/v) PEG 3350, 175 mM MgCl2, and 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9793
SYNCHROTRONNSLS X29A20.9792
SYNCHROTRONNSLS X29A30.95
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 26, 2007
ADSC QUANTUM 3152CCDOct 26, 2007
ADSC QUANTUM 3153CCDOct 26, 2007
RadiationMonochromator: Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97921
30.951
ReflectionRedundancy: 13.6 % / Number: 412989 / Rmerge(I) obs: 0.112 / Χ2: 1.01 / D res high: 2.33 Å / D res low: 50 Å / Num. obs: 30428 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.025099.710.0470.56712.4
3.985.0210010.0550.63613.6
3.483.9810010.0760.83411
3.163.4810010.1060.9313.9
2.943.1610010.1571.02614.3
2.762.9410010.2351.11314.4
2.622.7610010.3351.26114.3
2.512.6210010.4321.22114.4
2.412.5110010.531.23814.4
2.332.4194.910.631.22913.1
ReflectionResolution: 2.3→50 Å / Num. obs: 31529 / Redundancy: 13.5 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHARPphasing
SOLOMONphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8062 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 3166 10 %RANDOM
Rwork0.2223 ---
obs-31529 100 %-
Solvent computationBsol: 33.0966 Å2
Displacement parametersBiso max: 102.75 Å2 / Biso mean: 41.485 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.027 Å20 Å20 Å2
2--0.027 Å20 Å2
3----0.055 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 12 271 4843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.303
X-RAY DIFFRACTIONc_mcbond_it1.4021.5
X-RAY DIFFRACTIONc_scbond_it2.2052
X-RAY DIFFRACTIONc_mcangle_it2.3042
X-RAY DIFFRACTIONc_scangle_it3.3032.5
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
2.3-2.320.3609670.2432562629
2.32-2.330.3123440.2461574618
2.33-2.350.354540.2571556610
2.35-2.360.2964730.2481533606
2.36-2.380.3016550.2586573628
2.38-2.40.3327700.2603539609
2.4-2.420.2892760.2441550626
2.42-2.440.2854640.2555573637
2.44-2.460.264670.2168545612
2.46-2.480.2946720.2557543615
2.48-2.50.429470.2703556603
2.5-2.520.3203690.2764558627
2.52-2.540.3329480.2552579627
2.54-2.570.3643600.2541545605
2.57-2.590.293710.2449573644
2.59-2.620.3282620.2689539601
2.62-2.640.3402640.2814563627
2.64-2.670.3131610.2528561622
2.67-2.70.3063670.2623548615
2.7-2.730.3792690.2836550619
2.73-2.760.3128670.2602551618
2.76-2.790.3192690.234551620
2.79-2.820.2564710.2439572643
2.82-2.860.2978580.2425564622
2.86-2.90.3382570.2521556613
2.9-2.940.2949700.2449550620
2.94-2.980.2928610.2531570631
2.98-3.020.3459620.2459562624
3.02-3.070.2733580.2377572630
3.07-3.120.2706520.241573625
3.12-3.180.2984720.2378542614
3.18-3.230.2898610.2442568629
3.23-3.30.3268590.2446586645
3.3-3.360.2322550.2148561616
3.36-3.440.3203810.229560641
3.44-3.520.2427640.2313560624
3.52-3.60.3076590.2207584643
3.6-3.70.3116700.2472555625
3.7-3.810.2203550.2071577632
3.81-3.930.2365620.2133577639
3.93-4.070.2258770.1825572649
4.07-4.240.2169710.1774562633
4.24-4.430.2289620.1774587649
4.43-4.660.2708490.182586635
4.66-4.950.181610.1697589650
4.95-5.340.1817700.1613572642
5.34-5.870.3038520.2157608660
5.87-6.720.2196580.2044610668
6.72-8.460.2397740.1846608682
8.46-500.2622690.2256658727
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

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