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- PDB-2brf: Crystal Structure of the FHA Domain of Human Polynucleotide Kinas... -

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Basic information

Entry
Database: PDB / ID: 2brf
TitleCrystal Structure of the FHA Domain of Human Polynucleotide Kinase 3' Phosphatase
ComponentsBIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
KeywordsHYDROLASE/TRANSFERASE / FHA / FORKHEAD-ASSOCIATED / PNKP / PNK / POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA REPAIR / BER / SSBR / DSBR / XRCC1 / XRCC4 HYDROLASE / TRANSFERASE / BIFUNCTIONAL / HYDROLASE-TRANSFERASE complex
Function / homology
Function and homology information


purine nucleotide binding / polynucleotide 3'-phosphatase / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / positive regulation of double-strand break repair via nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / positive regulation of telomere maintenance / regulation of DNA repair / site of DNA damage ...purine nucleotide binding / polynucleotide 3'-phosphatase / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / positive regulation of double-strand break repair via nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / positive regulation of telomere maintenance / regulation of DNA repair / site of DNA damage / base-excision repair, gap-filling / nucleotide-excision repair / response to radiation / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / site of double-strand break / response to oxidative stress / double-stranded DNA binding / endonuclease activity / damaged DNA binding / DNA repair / nucleolus / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA / AAA domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 ...Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA / AAA domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / HAD superfamily / HAD-like superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOliver, A.W. / Ali, A.A.E. / Pearl, L.H.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Specific Recognition of a Multiply Phosphorylated Motif in the DNA Repair Scaffold Xrcc1 by the Fha Domain of Human Pnk.
Authors: Ali, A.A.E. / Jukes, R.M. / Pearl, L.H. / Oliver, A.W.
History
DepositionMay 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0013
Polymers11,8091
Non-polymers1922
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.812, 40.047, 37.512
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE / FHA DOMAIN OF POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE ...FHA DOMAIN OF POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE 5'-HYDROXYL-KINASE / POLYNUCLEOTIDE 3'-PHOSPHATASE


Mass: 11809.350 Da / Num. of mol.: 1 / Fragment: FHA DOMAIN, RESIDUES 1-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MODIFIED PET-17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 (DE3) PLYSS
References: UniProt: Q96T60, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: 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 Å3/Da / Density % sol: 37.6 %
Crystal growDetails: PROTEIN WAS CRYSTALLISED IN 0.1 M TRIS-HCL PH 8.5, 2.0 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→37.5 Å / Num. obs: 16490 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.9
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.9 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UJX

1ujx


Resolution: 1.4→37.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.811 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 834 5.1 %RANDOM
Rwork0.15 ---
obs0.152 15643 88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.02 Å2
2--0.06 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 10 143 908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.022792
X-RAY DIFFRACTIONr_bond_other_d0.0020.02751
X-RAY DIFFRACTIONr_angle_refined_deg2.5122.0211087
X-RAY DIFFRACTIONr_angle_other_deg1.06831746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93223.44829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40315126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.591157
X-RAY DIFFRACTIONr_chiral_restr0.1870.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02864
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02141
X-RAY DIFFRACTIONr_nbd_refined0.2450.2120
X-RAY DIFFRACTIONr_nbd_other0.2070.2728
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2387
X-RAY DIFFRACTIONr_nbtor_other0.0890.2514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4450.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1041.5639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.232824
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6713317
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.684.5261
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 21
Rwork0.185 595

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