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- PDB-1rc8: T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA -

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Basic information

Entry
Database: PDB / ID: 1rc8
TitleT4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA
Components
  • 5'-D(*GP*TP*CP*AP*C)-3'
  • Polynucleotide kinase
KeywordsTRANSFERASE/DNA / KINASE / PHOSPHATASE / ALPHA/BETA / P-LOOP / ssDNA / TRANSFERASE-DNA 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, 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
ADENOSINE-5'-DIPHOSPHATE / DNA / Polynucleotide kinase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsEastberg, J.H. / Pelletier, J. / Stoddard, B.L.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
Authors: Eastberg, J.H. / Pelletier, J. / Stoddard, B.L.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 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
B: 5'-D(*GP*TP*CP*AP*C)-3'
A: Polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2605
Polymers36,7152
Non-polymers5453
Water1,06359
1
B: 5'-D(*GP*TP*CP*AP*C)-3'
A: Polynucleotide kinase
hetero molecules

B: 5'-D(*GP*TP*CP*AP*C)-3'
A: Polynucleotide kinase
hetero molecules

B: 5'-D(*GP*TP*CP*AP*C)-3'
A: Polynucleotide kinase
hetero molecules

B: 5'-D(*GP*TP*CP*AP*C)-3'
A: Polynucleotide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,04020
Polymers146,8588
Non-polymers2,18212
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Unit cell
Length a, b, c (Å)82.170, 92.061, 123.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

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DNA chain / Protein , 2 types, 2 molecules BA

#1: DNA chain 5'-D(*GP*TP*CP*AP*C)-3'


Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Polynucleotide kinase / 2.7.1.78 / PNK / Polynucleotide 5'-hydroxyl- kinase


Mass: 35234.594 Da / Num. of mol.: 1
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: pAll17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase

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Non-polymers , 4 types, 62 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.51 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, Potassium Chloride, MES, Tris, ATP, DTT, EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2KCl11
3MES11
4TRIS11
5DTT11
6EDTA11
7KCl12
8MES12
9TRIS12
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Galburt, E.A., (2002) Structure, 10, 1249.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1droppH7.4
250 mM1dropKCl
31 mMdithiothreitol1drop
40.1 mMEDTA1drop
50.1 mMATP1drop
61 mg/mlprotein1drop
75-10 %PEG40001reservoir
80-5 mM1reservoirpH6.5
91

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2002
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 11117 / Num. obs: 11117 / % possible obs: 89.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.7
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 5 / % possible all: 91.6
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 5-6 / Num. measured all: 92826
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LTQ

1ltq


Resolution: 2.75→38.19 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 161032.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1112 10.3 %RANDOM
Rwork0.23 ---
all0.23 11117 --
obs0.23 10827 86.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4922 Å2 / ksol: 0.328913 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2--7.46 Å20 Å2
3----5.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.75→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 58 22 59 2436
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.471.5
X-RAY DIFFRACTIONc_mcangle_it10.032
X-RAY DIFFRACTIONc_scbond_it7.912
X-RAY DIFFRACTIONc_scangle_it11.462.5
LS refinement shellHighest resolution: 2.75 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork1493 -
Rfree-12.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMLIGAND.TOP
X-RAY DIFFRACTION4LIGAND.PARAMWATER.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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