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- PDB-3kt9: Aprataxin FHA Domain -

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Basic information

Entry
Database: PDB / ID: 3kt9
TitleAprataxin FHA Domain
ComponentsAprataxin
KeywordsHYDROLASE / FHA domain / beta sandwich / beta sheet / AMP hydrolase / Alternative splicing / Disease mutation / DNA damage / DNA repair / DNA-binding / Metal-binding / Neurodegeneration / Nucleus / Zinc / Zinc-finger
Function / homology
Function and homology information


adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / polynucleotide 3'-phosphatase activity / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / : / single strand break repair / mismatched DNA binding ...adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / polynucleotide 3'-phosphatase activity / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / : / single strand break repair / mismatched DNA binding / DNA ligation / phosphoprotein binding / regulation of protein stability / response to hydrogen peroxide / double-stranded RNA binding / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / DNA damage response / chromatin binding / chromatin / nucleolus / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Aprataxin, C2HE/C2H2/C2HC zinc finger / C2HE / C2H2 / C2HC zinc-binding finger / Scavenger mRNA decapping enzyme C-term binding / PNK, FHA domain / FHA domain / Tumour Suppressor Smad4 - #20 / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. ...: / Aprataxin, C2HE/C2H2/C2HC zinc finger / C2HE / C2H2 / C2HC zinc-binding finger / Scavenger mRNA decapping enzyme C-term binding / PNK, FHA domain / FHA domain / Tumour Suppressor Smad4 - #20 / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily / Tumour Suppressor Smad4 / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Aprataxin / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCherry, A.L. / Smerdon, S.J.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response.
Authors: Becherel, O.J. / Jakob, B. / Cherry, A.L. / Gueven, N. / Fusser, M. / Kijas, A.W. / Peng, C. / Katyal, S. / McKinnon, P.J. / Chen, J. / Epe, B. / Smerdon, S.J. / Taucher-Scholz, G. / Lavin, M.F.
History
DepositionNov 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aprataxin


Theoretical massNumber of molelcules
Total (without water)11,7901
Polymers11,7901
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.949, 40.554, 42.477
Angle α, β, γ (deg.)90.000, 110.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-182-

HOH

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Components

#1: Protein Aprataxin / Forkhead-associated domain histidine triad-like protein / FHA-HIT


Mass: 11789.759 Da / Num. of mol.: 1 / Fragment: FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APTX, AXA1 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q5T784, UniProt: Q7Z2E3*PLUS, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium fluoride, PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2007 / Details: Osmic Confocal optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. obs: 11553 / % possible obs: 90.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.052 / Χ2: 1.076 / Net I/σ(I): 19.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.722.80.29910181.17363.6
1.72-1.824.10.2313951.14288.2
1.82-1.9350.17514741.13391.2
1.93-2.085.50.11814581.13493.4
2.08-2.295.60.08215101.06593.7
2.29-2.625.60.06315211.08295.4
2.62-3.295.60.04515671.04896.8
3.29-155.50.03416100.94898.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.531 / Cor.coef. Fo:Fc: 0.311 / Cor.coef. Io to Ic: 0.301
Highest resolutionLowest resolution
Rotation2.8 Å100 Å
Translation2.8 Å8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.828 / SU B: 2.276 / SU ML: 0.078 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 568 4.9 %RANDOM
Rwork0.205 ---
obs0.206 11548 90.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 52.35 Å2 / Biso mean: 19.98 Å2 / Biso min: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.11 Å2
2---0.2 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 0 165 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022836
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9661126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66824.35939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2515166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.605157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02614
X-RAY DIFFRACTIONr_nbd_refined0.1630.2359
X-RAY DIFFRACTIONr_nbtor_refined0.2930.2555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2133
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.230
X-RAY DIFFRACTIONr_mcbond_it0.4221.5529
X-RAY DIFFRACTIONr_mcangle_it0.7372832
X-RAY DIFFRACTIONr_scbond_it0.9943346
X-RAY DIFFRACTIONr_scangle_it1.7134.5294
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 29 -
Rwork0.417 501 -
all-530 -
obs--55.56 %

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