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- PDB-2orv: human Thymidine Kinase 1 in complex with TP4A -

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Basic information

Entry
Database: PDB / ID: 2orv
Titlehuman Thymidine Kinase 1 in complex with TP4A
ComponentsThymidine kinase
KeywordsTRANSFERASE / TK-1 (THYMIDINE KINASE 1) / TP4A (P1-(5'-ADENOSYL)P4-(5'-(2'DEOXYTHYMIDIL))TETRAPHOSPHATE
Function / homology
Function and homology information


DNA synthesis involved in mitotic DNA replication / thymidine biosynthetic process / thymidine metabolic process / thymidine kinase / thymidine kinase activity / Pyrimidine salvage / nucleobase-containing compound metabolic process / G1/S-Specific Transcription / protein homotetramerization / phosphorylation ...DNA synthesis involved in mitotic DNA replication / thymidine biosynthetic process / thymidine metabolic process / thymidine kinase / thymidine kinase activity / Pyrimidine salvage / nucleobase-containing compound metabolic process / G1/S-Specific Transcription / protein homotetramerization / phosphorylation / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4TA / Thymidine kinase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSegura-Pena, D. / Lutz, S. / Monnerjahn, C. / Konrad, M. / Lavie, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Binding of ATP to TK1-like Enzymes Is Associated with a Conformational Change in the Quaternary Structure.
Authors: Segura-Pena, D. / Lutz, S. / Monnerjahn, C. / Konrad, M. / Lavie, A.
History
DepositionFeb 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5136
Polymers50,7672
Non-polymers1,7464
Water2,882160
1
A: Thymidine kinase
B: Thymidine kinase
hetero molecules

A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,02512
Polymers101,5344
Non-polymers3,4918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area11890 Å2
ΔGint-72 kcal/mol
Surface area25460 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.980, 80.980, 156.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 18 - 191 / Label seq-ID: 18 - 191

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein Thymidine kinase /


Mass: 25383.578 Da / Num. of mol.: 2 / Mutation: K203A, E204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TK1 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(D3) / References: UniProt: P04183, thymidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4TA / P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE


Type: RNA linking / Mass: 807.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O20P4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 2.8 M NaCl, 0.1M MES, 0.1M NaH2PO4, 0.1M KH2PO4, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.072 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Mar 17, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.08→19.5 Å / Num. all: 36463 / Num. obs: 34789 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 49.199 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.54
Reflection shellResolution: 2.08→2.21 Å / Redundancy: 3.18 % / Mean I/σ(I) obs: 2.3 / Num. measured obs: 14395 / Num. unique all: 4526 / Rsym value: 0.354 / % possible all: 79

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
XDSdata scaling
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.168 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.219 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2604 9.9 %RANDOM
Rwork0.197 ---
all0.202 23587 --
obs0.202 26191 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.246 Å2
Baniso -1Baniso -2Baniso -3
1-4.13 Å22.06 Å20 Å2
2--4.13 Å20 Å2
3----6.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 68 160 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222583
X-RAY DIFFRACTIONr_angle_refined_deg1.8112.0083493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55723.398103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74715452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9811519
X-RAY DIFFRACTIONr_chiral_restr0.1220.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021865
X-RAY DIFFRACTIONr_nbd_refined0.2340.21207
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21751
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.27
X-RAY DIFFRACTIONr_mcbond_it0.9381.51640
X-RAY DIFFRACTIONr_mcangle_it1.63222554
X-RAY DIFFRACTIONr_scbond_it2.12731060
X-RAY DIFFRACTIONr_scangle_it3.3574.5939
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1228 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.210.5
MEDIUM THERMAL0.742
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 184 -
Rwork0.284 1768 -
obs-1952 100 %

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