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Yorodumi- PDB-2wwg: Plasmodium falciparum thymidylate kinase in complex with dGMP and ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wwg | ||||||
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Title | Plasmodium falciparum thymidylate kinase in complex with dGMP and ADP | ||||||
Components | THYMIDILATE KINASE, PUTATIVE | ||||||
Keywords | TRANSFERASE / KINASE / MALARIA | ||||||
Function / homology | Function and homology information T2-induced deoxynucleotide kinase activity / guanylate kinase / dUDP biosynthetic process / guanylate kinase activity / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process ...T2-induced deoxynucleotide kinase activity / guanylate kinase / dUDP biosynthetic process / guanylate kinase activity / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Whittingham, J.L. / Carrero-Lerida, J. / Brannigan, J.A. / Ruiz-Perez, L.M. / Silva, A.P. / Fogg, M.J. / Wilkinson, A.J. / Gilbert, I.H. / Wilson, K.S. / Gonzalez-Pacanowska, D. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Structural Basis for the Efficient Phosphorylation of Aztmp and Dgmp by Plasmodium Falciparum Type I Thymidylate Kinase. Authors: Whittingham, J.L. / Carrero-Lerida, J. / Brannigan, J.A. / Ruiz-Perez, L.M. / Silva, A.P. / Fogg, M.J. / Wilkinson, A.J. / Gilbert, I.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 | 2wwg.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwg.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwg ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwg | HTTPS FTP |
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-Related structure data
Related structure data | 2wwfSC 2wwhC 2wwiC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 24950.326 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: 3D7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I4S1, dTMP kinase |
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-Non-polymers , 5 types, 207 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-GOL / #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: 2.98 Å3/Da / Density % sol: 58.6 % Description: STRUCTURE OF TMP-ADP COMPLEX USED AS STARTING MODEL |
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Crystal grow | pH: 7.5 Details: 4 MM HEPES PH 7.5, 1.32 M TRI- SODIUM CITRATE, 80 MM NACL, 3 % XYLITOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 33557 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WWF Resolution: 2.4→95.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.098 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.265 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.421 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→95.9 Å
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