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- PDB-2v54: Crystal structure of vaccinia virus thymidylate kinase bound to TDP -

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Basic information

Entry
Database: PDB / ID: 2v54
TitleCrystal structure of vaccinia virus thymidylate kinase bound to TDP
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS / ATP-BINDING / NUCLEOTIDE-BINDING / KINASE / POXVIRUS / TMP KINASE
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / THYMIDINE-5'-DIPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesVACCINIA VIRUS COPENHAGEN
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCaillat, C. / Topalis, D. / Agrofoglio, L.A. / Pochet, S. / Balzarini, J. / Deville-Bonne, D. / Meyer, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal Structure of Poxvirus Thymidylate Kinase: An Unexpected Dimerization Has Implications for Antiviral Therapy
Authors: Caillat, C. / Topalis, D. / Agrofoglio, L.A. / Pochet, S. / Balzarini, J. / Deville-Bonne, D. / Meyer, P.
History
DepositionOct 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4926
Polymers46,4872
Non-polymers1,0054
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-49.11 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.770, 55.590, 161.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THYMIDYLATE KINASE / / DTMP KINASE


Mass: 23243.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS COPENHAGEN / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) ROSETTA PLYSS / References: UniProt: P68693, dTMP kinase
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHYMIDINE-5'-DIPHOSPHATE (TYD): ALTERNATE CONFORMATION WITH POP 160 PYROPHOSPHATE (POP): ALTERNATE ...THYMIDINE-5'-DIPHOSPHATE (TYD): ALTERNATE CONFORMATION WITH POP 160 PYROPHOSPHATE (POP): ALTERNATE CONFORMATION WITH TYD 160

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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: 2.75 Å3/Da / Density % sol: 55.5 % / Description: NONE
Crystal growDetails: 23% PEG 400, 100 MM NA ACETATE, 100 MM MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 79520 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.25 / % possible all: 93.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2G

1e2g


Resolution: 2.4→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1024 5 %RANDOM
Rwork0.2163 ---
obs0.2163 20139 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.9287 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.569 Å20 Å20 Å2
2--10.451 Å20 Å2
3----11.021 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 60 107 3414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007289
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_deg1.32742
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 44 5 %
Rwork0.277 867 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DTDP_CNS.PARAMDTDP_CNS.TOPH
X-RAY DIFFRACTION5POP_CNS.PARAMPOP_CNS.TOPH

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