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- PDB-1ltq: CRYSTAL STRUCTURE OF T4 POLYNUCLEOTIDE KINASE -

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Basic information

Entry
Database: PDB / ID: 1ltq
TitleCRYSTAL STRUCTURE OF T4 POLYNUCLEOTIDE KINASE
ComponentsPOLYNUCLEOTIDE KINASE
KeywordsTRANSFERASE / KINASE / PHOSPHATASE / ALPHA/BETA / P-LOOP
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
ADENOSINE-5'-DIPHOSPHATE / Polynucleotide kinase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsGalburt, E.A. / Pelletier, J. / Wilson, G. / Stoddard, B.L.
CitationJournal: Structure / Year: 2002
Title: Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase.
Authors: Galburt, E.A. / Pelletier, J. / Wilson, G. / Stoddard, B.L.
History
DepositionMay 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7403
Polymers35,2351
Non-polymers5052
Water2,594144
1
A: POLYNUCLEOTIDE KINASE
hetero molecules

A: POLYNUCLEOTIDE KINASE
hetero molecules

A: POLYNUCLEOTIDE KINASE
hetero molecules

A: POLYNUCLEOTIDE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,96012
Polymers140,9384
Non-polymers2,0218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area11900 Å2
ΔGint-69 kcal/mol
Surface area52970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.585, 93.684, 124.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein POLYNUCLEOTIDE KINASE / 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P06855, polynucleotide 5'-hydroxyl-kinase
#2: 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
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
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
Crystal grow
*PLUS
pH: 7.4
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 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97873 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002
RadiationMonochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97873 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 38288 / Num. obs: 38288 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 5.7 / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. measured all: 191084 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.288

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2735 7 %RANDOM
Rwork0.236 ---
all0.238 37037 --
obs0.238 37037 --
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 31 144 2524
Refinement
*PLUS
Rfactor all: 0.238 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.4

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