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- PDB-1w4r: Structure of a type II thymidine kinase with bound dTTP -

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Basic information

Entry
Database: PDB / ID: 1w4r
TitleStructure of a type II thymidine kinase with bound dTTP
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / TYPE II
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
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / THYMIDINE-5'-TRIPHOSPHATE / Thymidine kinase, cytosolic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsBirringer, M.S. / Claus, M.T. / Folkers, G. / Kloer, D.P. / Schulz, G.E. / Scapozza, L.
CitationJournal: FEBS Lett. / Year: 2005
Title: Structure of a Type II Thymidine Kinase with Bound Dttp
Authors: Birringer, M.S. / Claus, M.T. / Folkers, G. / Kloer, D.P. / Schulz, G.E. / Scapozza, L.
History
DepositionJul 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDINE KINASE
B: THYMIDINE KINASE
C: THYMIDINE KINASE
D: THYMIDINE KINASE
E: THYMIDINE KINASE
F: THYMIDINE KINASE
G: THYMIDINE KINASE
H: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,84225
Polymers174,3078
Non-polymers4,53517
Water14,304794
1
A: THYMIDINE KINASE
B: THYMIDINE KINASE
C: THYMIDINE KINASE
D: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,34412
Polymers87,1544
Non-polymers2,1908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-16.2 kcal/mol
Surface area31630 Å2
MethodPISA
2
E: THYMIDINE KINASE
F: THYMIDINE KINASE
G: THYMIDINE KINASE
H: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49813
Polymers87,1544
Non-polymers2,3459
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-29.7 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.496, 122.920, 115.274
Angle α, β, γ (deg.)90.00, 130.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.545498, -0.763843, 0.344928), (-0.755071, 0.269291, -0.597788), (0.36373, -0.586537, -0.723653)113.444, 83.061, 32.641
3given(-0.873078, 0.2695, 0.406331), (0.262291, -0.442909, 0.857342), (0.411021, 0.855103, 0.316007)41.843, 107.866, -83.117
4given(0.424704, 0.487538, -0.762845), (0.485981, -0.833694, -0.262254), (-0.763838, -0.259348, -0.591008)-20.772, 130.299, 44.409
5given(-0.261718, -0.138417, -0.955167), (0.112513, -0.98729, 0.112243), (-0.958564, -0.078093, 0.273966)90.743, 137.546, -4.79
6given(-0.28316, 0.790217, 0.543486), (0.798022, -0.120184, 0.590522), (0.531959, 0.600926, -0.59658)-42.478, 54.693, -13.331
7given(-0.141097, -0.171068, 0.975104), (-0.942272, 0.32533, -0.079272), (-0.303669, -0.929998, -0.207096)-2.741, 68.107, 70.162
8given(0.674675, -0.480474, -0.56032), (0.032427, 0.777684, -0.627819), (0.737402, 0.405404, 0.540264)88.57, 60.826, -57.872

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Components

#1: Protein
THYMIDINE KINASE /


Mass: 21788.426 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04183, thymidine kinase
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT CONSISTS OF RESIDUES 15-194 OF THE NATIVE PROTEIN PLUS AN N-TERMINAL EXTENSION OF 15 ...CONSTRUCT CONSISTS OF RESIDUES 15-194 OF THE NATIVE PROTEIN PLUS AN N-TERMINAL EXTENSION OF 15 RESIDUES CONTAINING A HIS6-TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.2 / Details: pH 7.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794, 1.277, 0.9196
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
21.2771
30.91961
ReflectionResolution: 1.83→40 Å / Num. obs: 140080 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 1.83→1.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 7.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 7423 5 %RANDOM
Rwork0.159 ---
obs0.16 140080 99 %-
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10106 0 248 794 11148

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