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- PDB-1yjm: Crystal structure of the FHA domain of mouse polynucleotide kinas... -

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Basic information

Entry
Database: PDB / ID: 1yjm
TitleCrystal structure of the FHA domain of mouse polynucleotide kinase in complex with an XRCC4-derived phosphopeptide.
Components
  • 12-mer peptide from DNA-repair protein XRCC4
  • Polynucleotide 5'-hydroxyl-kinase
KeywordsTransferase/DNA BINDING PROTEIN / polynucleotide kinase / FHA domain / XRCC4 phosphopeptide / Transferase-DNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping ...polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping / ubiquitin-like ligase-substrate adaptor activity / positive regulation of telomere maintenance via telomerase / double-strand break repair via nonhomologous end joining / site of double-strand break / double-stranded DNA binding / response to oxidative stress / phosphorylation / DNA repair / DNA damage response / nucleolus / nucleoplasm / ATP binding / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. ...Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. / Durocher, D. / Weinfeld, M. / Glover, J.N.M.
CitationJournal: Mol.Cell / Year: 2005
Title: The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.
Authors: Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. / Durocher, D. / Weinfeld, M. / Glover, J.N.
History
DepositionJan 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polynucleotide 5'-hydroxyl-kinase
B: Polynucleotide 5'-hydroxyl-kinase
C: Polynucleotide 5'-hydroxyl-kinase
E: 12-mer peptide from DNA-repair protein XRCC4
F: 12-mer peptide from DNA-repair protein XRCC4
G: 12-mer peptide from DNA-repair protein XRCC4


Theoretical massNumber of molelcules
Total (without water)40,1016
Polymers40,1016
Non-polymers00
Water3,387188
1
A: Polynucleotide 5'-hydroxyl-kinase
E: 12-mer peptide from DNA-repair protein XRCC4


Theoretical massNumber of molelcules
Total (without water)13,3672
Polymers13,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area6350 Å2
MethodPISA
2
B: Polynucleotide 5'-hydroxyl-kinase
F: 12-mer peptide from DNA-repair protein XRCC4


Theoretical massNumber of molelcules
Total (without water)13,3672
Polymers13,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-5 kcal/mol
Surface area6170 Å2
MethodPISA
3
C: Polynucleotide 5'-hydroxyl-kinase
G: 12-mer peptide from DNA-repair protein XRCC4


Theoretical massNumber of molelcules
Total (without water)13,3672
Polymers13,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-6 kcal/mol
Surface area5820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.155, 122.999, 136.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

21A-123-

HOH

DetailsThe biological unit is a monomer of full-length polynucleotide kinase.

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Components

#1: Protein Polynucleotide 5'-hydroxyl-kinase /


Mass: 11799.494 Da / Num. of mol.: 3 / Fragment: FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pnk / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold 99
References: UniProt: Q9JLV6, polynucleotide 5'-hydroxyl-kinase
#2: Protein/peptide 12-mer peptide from DNA-repair protein XRCC4 / X-ray repair cross-complementing protein 4


Mass: 1567.457 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: chemically synthesized phospho-peptide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Na citrate (pH 5.5), 25% PEG 4000, 0.2M Li2SO4, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2004
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 21246 / Num. obs: 18994 / % possible obs: 89.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rsym value: 0.051 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.194 / % possible all: 70.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The FHA domain from the full-length mouse PNK structure, 1YJ5

1yj5


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.338 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24278 1022 5.1 %RANDOM
Rwork0.21088 ---
all0.21253 21246 --
obs0.21253 18994 89.49 %-
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 mean: 25.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 0 188 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222582
X-RAY DIFFRACTIONr_bond_other_d0.0010.022407
X-RAY DIFFRACTIONr_angle_refined_deg0.8622.0223526
X-RAY DIFFRACTIONr_angle_other_deg0.66935603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54823.96101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99715407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4021520
X-RAY DIFFRACTIONr_chiral_restr0.0550.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
X-RAY DIFFRACTIONr_nbd_refined0.1630.2349
X-RAY DIFFRACTIONr_nbd_other0.1490.22311
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21169
X-RAY DIFFRACTIONr_nbtor_other0.070.21586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0820.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1010.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1921.52124
X-RAY DIFFRACTIONr_mcbond_other0.0221.5679
X-RAY DIFFRACTIONr_mcangle_it0.20822667
X-RAY DIFFRACTIONr_scbond_it0.28231052
X-RAY DIFFRACTIONr_scangle_it0.434.5859
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 63 -
Rwork0.253 1085 -
obs--71.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3170.15010.00541.4649-0.26761.7753-0.0265-0.0734-0.02320.0350.05590.0057-0.07390.0262-0.0295-0.0768-0.00030.0074-0.05140.0198-0.040917.30611.33458.95
21.15240.16990.02181.3144-0.01881.76870.04030.01510.04530.051-0.1182-0.05-0.0999-0.01210.0779-0.0665-0.0258-0.0135-0.05950.0125-0.034329.7824.87547.417
32.0791-0.2964-0.05662.3950.1612.02270.0647-0.0035-0.0942-0.0664-0.00720.0086-0.0791-0.0104-0.0574-0.04690.02880.0081-0.0947-0.0127-0.049311.07313.19182.458
45.80142.31352.62256.1495-2.90654.174-0.07470.32770.13730.1242-0.13340.18740.3668-0.6540.2081-0.1590.0342-0.05550.02860.095-0.05270.22310.17251.187
56.24931.99051.09344.3058-0.61915.5404-0.02480.3077-0.1632-0.148-0.0486-0.74730.21460.38640.0734-0.16550.0561-0.0145-0.02970.10470.029547.02217.83345.583
65.42656.89363.69648.75724.69572.5179-1.1859-0.0104-0.2821-1.45010.3537-0.08611.3998-1.69810.83220.05410.0481-0.0970.1802-0.01850.05631.2593.74870.917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1105 - 110
2X-RAY DIFFRACTION2BB6 - 1106 - 110
3X-RAY DIFFRACTION3CC7 - 1077 - 107
4X-RAY DIFFRACTION4ED3 - 101 - 7
5X-RAY DIFFRACTION5FE3 - 101 - 7
6X-RAY DIFFRACTION6GF3 - 81 - 5

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