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- PDB-2ia5: T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium. -

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Basic information

Entry
Database: PDB / ID: 2ia5
TitleT4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.
ComponentsPolynucleotide kinase
KeywordsTRANSFERASE / Polynucleotide Kinase Phosphatase Sulfate-Complex
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 phosphatase domain / Polynucleotide kinase PNKP, C-terminal phosphatase domain / AAA domain / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...: / Polynucleotide kinase PNKP phosphatase domain / Polynucleotide kinase PNKP, C-terminal phosphatase domain / AAA domain / 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
ARSENIC / Polynucleotide kinase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhu, H. / Smith, P.C. / Wang, L.K. / Lima, C.D. / Shuman, S.
CitationJournal: Virology / Year: 2007
Title: Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase.
Authors: Zhu, H. / Smith, P. / Wang, L.K. / Shuman, S.
History
DepositionSep 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Aug 30, 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_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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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: Polynucleotide kinase
B: Polynucleotide kinase
C: Polynucleotide kinase
D: Polynucleotide kinase
E: Polynucleotide kinase
F: Polynucleotide kinase
G: Polynucleotide kinase
H: Polynucleotide kinase
I: Polynucleotide kinase
J: Polynucleotide kinase
K: Polynucleotide kinase
L: Polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)420,51566
Polymers416,06212
Non-polymers4,45354
Water17,583976
1
A: Polynucleotide kinase
B: Polynucleotide kinase
C: Polynucleotide kinase
D: Polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,23724
Polymers138,6874
Non-polymers1,55020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-299 kcal/mol
Surface area54700 Å2
MethodPISA
2
E: Polynucleotide kinase
F: Polynucleotide kinase
G: Polynucleotide kinase
H: Polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,18822
Polymers138,6874
Non-polymers1,50118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-283 kcal/mol
Surface area55190 Å2
MethodPISA
3
I: Polynucleotide kinase
J: Polynucleotide kinase
K: Polynucleotide kinase
L: Polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,08920
Polymers138,6874
Non-polymers1,40216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-268 kcal/mol
Surface area54500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.630, 128.050, 357.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsBiological unit is a homo-tetramer. The ASU contains three such tetramers.

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Components

#1: Protein
Polynucleotide kinase / PNK / Polynucleotide 5'-hydroxy-kinase


Mass: 34671.855 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: pseT / Plasmid: pET28-His10-Smt3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: As
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 976 / 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: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 100mM Sodium cacodylate, 12% PEG-8000, 0.2 M ammonium sulfate, 20 mM urea, 5 mM DTT, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2002
Details: Double crystal monochromator with sagitally focusing Si(111) crystals
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 126336 / Num. obs: 124693 / % possible obs: 98.7 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 4.32 % / Biso Wilson estimate: 71.8 Å2 / Rsym value: 0.104 / Net I/σ(I): 12.01
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.57 / Num. unique all: 6245 / Rsym value: 0.535

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1LTQ dimer

1ltq


Resolution: 2.9→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1948026.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2835 2.5 %RANDOM
Rwork0.24 ---
obs0.24 111683 88 %-
all-126245 --
Solvent computationSolvent model: FLAT MODEL / Bsol: -0.445649 Å2 / ksol: 0.24 e/Å3
Displacement parametersBiso mean: 60.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--24.83 Å20 Å2
3----23.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28415 0 198 976 29589
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.151
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.263
X-RAY DIFFRACTIONc_mcangle_it7.024
X-RAY DIFFRACTIONc_scbond_it5.74
X-RAY DIFFRACTIONc_scangle_it8.815
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.436 207 2.5 %
Rwork0.405 8085 -
obs--66.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ps_param.hackps_topo.hack
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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