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- PDB-3zvl: The structural basis for substrate recognition by mammalian polyn... -

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Basic information

Entry
Database: PDB / ID: 3zvl
TitleThe structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase
ComponentsBIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
KeywordsHYDROLASE/TRANSFERASE / HYDROLASE-TRANSFERASE COMPLEX / BASE EXCISION REPAIR / BER / NON-HOMOLOGOUS END-JOINING / NHEJ / DNA REPAIR / CANCER
Function / homology
Function and homology information


polynucleotide 3'-phosphatase / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / SCF ubiquitin ligase complex / protein K63-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / double-strand break repair via nonhomologous end joining / site of double-strand break ...polynucleotide 3'-phosphatase / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / SCF ubiquitin ligase complex / protein K63-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA damage response / 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 / SMAD/FHA domain superfamily / HAD superfamily/HAD-like ...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 / SMAD/FHA domain superfamily / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGarces, F. / Pearl, L.H. / Oliver, A.W.
CitationJournal: Mol.Cell / Year: 2011
Title: The Structural Basis for Substrate Recognition by Mammalian Polynucleotide Kinase 3' Phosphatase.
Authors: Garces, F. / Pearl, L.H. / Oliver, A.W.
History
DepositionJul 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,90316
Polymers45,9481
Non-polymers95515
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.750, 63.500, 67.900
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE KINASE-3'-PHOSPHATASE / PNKP


Mass: 45948.227 Da / Num. of mol.: 1
Fragment: POLYNUCLEOTIDE 3'-PHOSPHATASE AND POLYNUCLEOTIDE 5'-HYDROXYL-KINASE DOMAINS, RESIDUES 111-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA2 (DE3) PLYSS
References: UniProt: Q9JLV6, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase

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Non-polymers , 5 types, 523 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 0.05 M NACACODYLATE PH 6.5, 0.2 M AMMONIUM ACETATE, 0.01 M MG ACETATE, 30 % (W/V) PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→33.93 Å / Num. obs: 39354 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.97 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 58.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YJ5

1yj5


Resolution: 1.65→33.933 Å / SU ML: 0.2 / σ(F): 0.84 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 3839 5 %
Rwork0.1705 --
obs0.1729 76395 88.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.337 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9467 Å20 Å21.6274 Å2
2--3.5224 Å20 Å2
3----2.5757 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 57 508 3481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063099
X-RAY DIFFRACTIONf_angle_d1.0264217
X-RAY DIFFRACTIONf_dihedral_angle_d15.9921137
X-RAY DIFFRACTIONf_chiral_restr0.069458
X-RAY DIFFRACTIONf_plane_restr0.005557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.7090.29352200.25544427X-RAY DIFFRACTION54
1.709-1.77750.30272800.24325720X-RAY DIFFRACTION70
1.7775-1.85830.26744140.22027553X-RAY DIFFRACTION93
1.8583-1.95630.26224130.18697746X-RAY DIFFRACTION95
1.9563-2.07890.21724200.17287779X-RAY DIFFRACTION96
2.0789-2.23930.2314310.15977859X-RAY DIFFRACTION96
2.2393-2.46460.2123970.16057870X-RAY DIFFRACTION96
2.4646-2.82110.21894210.16537909X-RAY DIFFRACTION97
2.8211-3.55370.21554270.15457890X-RAY DIFFRACTION97
3.5537-33.940.17534160.14927803X-RAY DIFFRACTION96

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