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- PDB-2wwg: Plasmodium falciparum thymidylate kinase in complex with dGMP and ADP -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wwg | ||||||
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Title | Plasmodium falciparum thymidylate kinase in complex with dGMP and ADP | ||||||
![]() | THYMIDILATE KINASE, PUTATIVE | ||||||
![]() | TRANSFERASE / KINASE / MALARIA | ||||||
Function / homology | ![]() T2-induced deoxynucleotide kinase activity / guanylate kinase / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity ...T2-induced deoxynucleotide kinase activity / guanylate kinase / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
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PDB format | ![]() | 120.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wwfSC ![]() 2wwhC ![]() 2wwiC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() Strain: 3D7 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 207 molecules ![](data/chem/img/DGP.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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Refine LS restraints |
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