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- PDB-2orw: Thermotoga maritima thymidine kinase 1 like enzyme in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2orw
TitleThermotoga maritima thymidine kinase 1 like enzyme in complex with TP4A
ComponentsThymidine kinase
KeywordsTRANSFERASE / TmTK / TP4A
Function / homology
Function and homology information


thymidine metabolic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / zinc ion binding / ATP binding / identical protein binding / 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
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1648
Polymers41,3702
Non-polymers1,7946
Water6,666370
1
A: Thymidine kinase
B: Thymidine kinase
hetero molecules

A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,32816
Polymers82,7404
Non-polymers3,58812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)102.550, 59.630, 61.440
Angle α, β, γ (deg.)90.00, 103.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thymidine kinase /


Mass: 20684.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tdk / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: Q9WYN2, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 65% 2-methyl-2,4-pentanediol (MPD), 0.1 M Na-Acetate, pH 5.0, 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 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2005 / Details: mirrors
RadiationMonochromator: SI (111) sagittal focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→28 Å / Num. all: 55419 / Num. obs: 55419 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 15.771 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.44
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8976 / Rsym value: 0.395 / % possible all: 88.7

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Phasing

Phasing MRRfactor: 0.42 / Cor.coef. Fo:Fc: 0.519
Highest resolutionLowest resolution
Rotation3 Å29.06 Å
Translation3 Å29.06 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.444 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 5566 10 %RANDOM
Rwork0.169 ---
all0.17275 55419 --
obs0.173 55418 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.06 Å2
2--1.09 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 106 370 3170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222843
X-RAY DIFFRACTIONr_angle_refined_deg1.7782.0293847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64224.732112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19515521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0421512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022004
X-RAY DIFFRACTIONr_nbd_refined0.1950.21430
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2324
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.228
X-RAY DIFFRACTIONr_mcbond_it1.071.51737
X-RAY DIFFRACTIONr_mcangle_it1.72322748
X-RAY DIFFRACTIONr_scbond_it2.76431238
X-RAY DIFFRACTIONr_scangle_it4.3864.51099
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 336 -
Rwork0.238 2964 -
obs-3300 78.18 %

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