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- PDB-1ly1: Structure and Mechanism of T4 Polynucleotide Kinase -

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Basic information

Entry
Database: PDB / ID: 1ly1
TitleStructure and Mechanism of T4 Polynucleotide Kinase
Componentspolynucleotide kinase
KeywordsTRANSFERASE / PNK / KINASE / PHOSPHATASE / POLYNUCLEOTIDE / T4 / PHAGE
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 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
Polynucleotide kinase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å
AuthorsWang, L.K. / Lima, C.D. / Shuman, S.
CitationJournal: EMBO J. / Year: 2002
Title: Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme.
Authors: Wang, L.K. / Lima, C.D. / Shuman, S.
History
DepositionJun 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The sulfate ions mimic substrate nucleotide phosphates.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0555
Polymers20,6711
Non-polymers3844
Water2,558142
1
A: polynucleotide kinase
hetero molecules

A: polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,11010
Polymers41,3422
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)65.300, 91.800, 67.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20670.787 Da / Num. of mol.: 1 / Fragment: kinase domain, residues 1-181
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: PET / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M NaOAc 4.6, 5mM DTT, 16% PEG2000MME, 0.4M AMSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
30.2 M1dropNaCl
40.3 Mimidazole1drop
510 %glycerol1drop
6100 mMsodium acetate1reservoirpH4.6
75 mMdithiothreitol1reservoir
816 %PEG2000 MME1reservoir
90.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2001
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 14453 / Num. obs: 12892 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.3
Reflection shellResolution: 2→2.06 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.3 / % possible all: 77.7
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. measured all: 36111 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 77.7 % / Rmerge(I) obs: 0.223

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIR / Resolution: 2→19.01 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 655 5 %RANDOM
Rwork0.21 ---
all-14121 --
obs-13119 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5142 Å2 / ksol: 0.38958 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å20 Å2
2--3.89 Å20 Å2
3----7.26 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→19.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 20 142 1403
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.292
X-RAY DIFFRACTIONc_scangle_it22.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 90 4.6 %
Rwork0.278 1868 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / Rfactor Rwork: 0.278

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