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- PDB-2w0s: Crystal structure of vaccinia virus thymidylate kinase bound to b... -

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Basic information

Entry
Database: PDB / ID: 2w0s
TitleCrystal structure of vaccinia virus thymidylate kinase bound to brivudin-5'-monophosphate
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
Chem-BVP / Thymidylate kinase
Similarity search - Component
Biological speciesVACCINIA VIRUS COPENHAGEN
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.918 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 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Version format compliance
Revision 1.2Dec 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_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.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: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01611
Polymers46,4872
Non-polymers1,5299
Water1086
1
A: THYMIDYLATE KINASE
hetero molecules

B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01611
Polymers46,4872
Non-polymers1,5299
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_454-x-1/2,-y,z-1/21
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-97.22 kcal/mol
Surface area17550 Å2
MethodPISA
2
A: THYMIDYLATE KINASE
hetero molecules

B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01611
Polymers46,4872
Non-polymers1,5299
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area4040 Å2
ΔGint-92.05 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.370, 78.350, 95.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:60 )
211CHAIN B AND (RESSEQ 2:60 )
112CHAIN A AND (RESSEQ 64:204 )
212CHAIN B AND (RESSEQ 64:204 )

NCS ensembles :
ID
1
2
DetailsTHIS ENTRY CONTAINS A SECONDARY BVP (BVP 1209) BINDING SITE THAT IS PRESENT AT THE DIMERIC INTERFACE.

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BVP / (E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / BVDU-MP


Type: DNA linking / Mass: 413.115 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H14BrN2O8P
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.2 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growDetails: 24% PEG 2000 MME, 100 MM TRIS-HCL PH 8.5, 5 MM MGCL2, 28 MM BVDU

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9198
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.92→49.75 Å / Num. obs: 69977 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 41.23 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.9
Reflection shellResolution: 2.92→3.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V54

2v54


Resolution: 2.918→36.852 Å / SU ML: 0.44 / σ(F): 1.45 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2828 1843 10.11 %
Rwork0.2124 --
obs0.2196 18237 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.359 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.6175 Å20 Å2-0 Å2
2--19.3659 Å20 Å2
3----11.7485 Å2
Refinement stepCycle: LAST / Resolution: 2.918→36.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 83 6 3319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013388
X-RAY DIFFRACTIONf_angle_d1.3614581
X-RAY DIFFRACTIONf_dihedral_angle_d21.7821253
X-RAY DIFFRACTIONf_chiral_restr0.082512
X-RAY DIFFRACTIONf_plane_restr0.005574
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A466X-RAY DIFFRACTIONPOSITIONAL
12B466X-RAY DIFFRACTIONPOSITIONAL0.052
21A1132X-RAY DIFFRACTIONPOSITIONAL
22B1132X-RAY DIFFRACTIONPOSITIONAL0.052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9177-2.99650.38971330.3071218X-RAY DIFFRACTION96
2.9965-3.08460.3241440.27731270X-RAY DIFFRACTION100
3.0846-3.18420.2851360.25721249X-RAY DIFFRACTION100
3.1842-3.29790.33691430.24151269X-RAY DIFFRACTION100
3.2979-3.42980.35161440.24181286X-RAY DIFFRACTION100
3.4298-3.58580.34581410.23491255X-RAY DIFFRACTION100
3.5858-3.77470.34751430.21041271X-RAY DIFFRACTION100
3.7747-4.01090.28281410.21071267X-RAY DIFFRACTION100
4.0109-4.32020.22771420.18711256X-RAY DIFFRACTION100
4.3202-4.75410.24491440.15771257X-RAY DIFFRACTION100
4.7541-5.44020.22191460.16121269X-RAY DIFFRACTION100
5.4402-6.84680.2531440.19081276X-RAY DIFFRACTION100
6.8468-36.85470.22951420.1781251X-RAY DIFFRACTION99

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