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Yorodumi- PDB-5fuy: catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fuy | ||||||
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Title | catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP | ||||||
Components | THYMDINE KINASE | ||||||
Keywords | TRANSFERASE / THYMIDINE KINASE / T.BRUCEI / TBTK / TKII / DTMP | ||||||
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: 2.8 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 | 5fuy.cif.gz | 204.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fuy.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fuy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fuy ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fuy | HTTPS FTP |
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-Related structure data
Related structure data | 5fuvSC 5fuwC 5fuxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20574.455 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 204-383 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: LISTER427 / Plasmid: 11347 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Variant (production host): SF9 / References: UniProt: Q38CF2, thymidine kinase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-QBT / [( #4: Chemical | ChemComp-ZN / #5: 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: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.15 M DL-MALIC ACID PH 7.0, 20% (W/V) PEG 3350, 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2, PLUS SEEDING |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→65.02 Å / Num. obs: 31168 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FUV Resolution: 2.8→152.22 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.383 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / 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: 65.494 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→152.22 Å
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