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- PDB-5uj0: Structure of T4Pnkp 3' phosphatase covalently bound to BeF3 -

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Basic information

Entry
Database: PDB / ID: 5uj0
TitleStructure of T4Pnkp 3' phosphatase covalently bound to BeF3
ComponentsPolynucleotide kinase
KeywordsTRANSFERASE / HYDROLASE / Phosphatase / BeF3-bound / Beryllium / Pnkp
Function / homology
Function and homology information


deoxynucleotide 3'-phosphatase / deoxynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / DNA repair / ATP binding
Similarity search - Function
Polynucleotide kinase PNKP, C-terminal phosphatase domain / AAA domain / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polynucleotide kinase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShuman, S. / Chatterjee, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM63611 United States
CitationJournal: To Be Published
Title: Truncated T4Pnk covalently bound to BeF3
Authors: Shuman, S. / Chatterjee, D.
History
DepositionJan 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polynucleotide kinase
B: Polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6675
Polymers33,5262
Non-polymers1413
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-30 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.790, 99.790, 194.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-509-

HOH

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Components

#1: Protein Polynucleotide kinase / PNK / Deoxynucleotide 3'-phosphatase / Polynucleotide 5'-hydroxyl-kinase


Mass: 16763.189 Da / Num. of mol.: 2 / Fragment: UNP residues 157-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: pseT / Plasmid: p28(smt) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase, deoxynucleotide 3'-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M (NH4)2SO4 and 0.1 M Tris-HCl (pH=7.5)

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.29→88.8 Å / Num. obs: 22056 / % possible obs: 99.5 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rsym value: 0.1 / Net I/σ(I): 16.2
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2043 / CC1/2: 0.786 / Rpim(I) all: 0.492 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LTQ

1ltq


Resolution: 2.3→88.753 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.2289 1122 5.09 %
Rwork0.1844 --
obs0.1867 22056 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→88.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 8 114 2367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082292
X-RAY DIFFRACTIONf_angle_d1.1543097
X-RAY DIFFRACTIONf_dihedral_angle_d13.389863
X-RAY DIFFRACTIONf_chiral_restr0.046343
X-RAY DIFFRACTIONf_plane_restr0.005389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40470.34011350.26752473X-RAY DIFFRACTION96
2.4047-2.53150.30971400.24652566X-RAY DIFFRACTION100
2.5315-2.69010.29441390.23632601X-RAY DIFFRACTION99
2.6901-2.89790.26631410.22992583X-RAY DIFFRACTION100
2.8979-3.18950.2281450.20982600X-RAY DIFFRACTION100
3.1895-3.6510.25631570.19082621X-RAY DIFFRACTION100
3.651-4.59990.18471290.14342669X-RAY DIFFRACTION100
4.5999-88.8190.18661360.16162821X-RAY DIFFRACTION100

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