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Yorodumi- PDB-3ngs: Structure of Leishmania nucleoside diphosphate kinase b with orde... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ngs | ||||||
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Title | Structure of Leishmania nucleoside diphosphate kinase b with ordered nucleotide-binding loop | ||||||
Components | Nucleoside diphosphate kinaseNucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / LmNDKb / phosphate ion / ordered nucleotide-binding loop | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / ciliary plasm / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Trindade, D.M. / Sousa, T.A.C.B. / Tonoli, C.C.C. / Santos, C.R. / Arni, R.K. / Ward, R.J. / Oliveira, A.H.C. / Murakami, M.T. | ||||||
Citation | Journal: Mol Biosyst / Year: 2011 Title: Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding. Authors: Souza, T.A. / Trindade, D.M. / Tonoli, C.C. / Santos, C.R. / Ward, R.J. / Arni, R.K. / Oliveira, A.H. / Murakami, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ngs.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ngs.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ngs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/3ngs ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ngs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16660.953 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: L1648.07, LmjF32.2950, NDKb / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9U1E1, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | ChemComp-DTT / | #4: 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: 3.58 Å3/Da / Density % sol: 65.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: sodium/potassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2010 |
Radiation | Monochromator: silicon double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.458 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→99 Å / Num. obs: 65810 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.7 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.801 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.693 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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