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Yorodumi- PDB-5fuv: catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fuv | |||||||||
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Title | catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd | |||||||||
Components | THYMDINE KINASE | |||||||||
Keywords | TRANSFERASE / THYMIDINE KINASE / T.BRUCEI / TBTK / TKII / DTHD | |||||||||
Function / homology | Function and homology information pyrimidine deoxyribonucleotide salvage / thymidine metabolic process / thymidine kinase / thymidine kinase activity / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / DNA biosynthetic process / phosphorylation / mitochondrion / ATP binding ...pyrimidine deoxyribonucleotide salvage / thymidine metabolic process / thymidine kinase / thymidine kinase activity / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / DNA biosynthetic process / phosphorylation / mitochondrion / ATP binding / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | TRYPANOSOMA BRUCEI (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Timm, J. / Valente, M. / Castillo-Acosta, V. / Balzarini, T. / Nettleship, J.E. / Rada, H. / Wilson, K.S. / Gonzalez-Pacanowska, D. | |||||||||
Citation | Journal: Mol.Microbiol. / Year: 2016 Title: Cell Cycle Regulation and Novel Structural Features of Thymidine Kinase, an Essential Enzyme in Trypanosoma Brucei. Authors: Valente, M. / Timm, J. / Castillo-Acosta, V.M. / Ruiz-Perez, L.M. / Balzarini, T. / Nettleship, J.E. / Bird, L.E. / Rada, H. / Wilson, K.S. / Gonzalez-Pacanowska, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fuv.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fuv.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fuv ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fuv | HTTPS FTP |
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-Related structure data
Related structure data | 5fuwC 5fuxC 5fuyC 1w4rS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20503.375 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 204-383 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Variant: LISTER427 / Plasmid: 11347 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q38CF2, thymidine kinase |
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-Non-polymers , 5 types, 94 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M HEPES PH 7.0, 0.8 M SUCCINIC ACID 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.25 Å / Num. obs: 31864 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W4R Resolution: 2.3→114.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.613 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.235 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→114.68 Å
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