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Yorodumi- PDB-3ngr: Crystal structure of Leishmania nucleoside diphosphate kinase b w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ngr | ||||||
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Title | Crystal structure of Leishmania nucleoside diphosphate kinase b with unordered nucleotide-binding loop. | ||||||
Components | Nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / NDKb / phosphate ion | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / ciliary plasm / CTP biosynthetic process / UTP 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: 2.95 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 | 3ngr.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ngr.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ngr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ngr_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 3ngr_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 3ngr_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 3ngr_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/3ngr ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ngr | HTTPS FTP |
-Related structure data
Related structure data | 3ngsC 3ngtC 3nguC 3prvC 1nskS 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
#1: Protein | Mass: 16660.953 Da / Num. of mol.: 1 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): BL21DE3 / References: UniProt: Q9U1E1, nucleoside-diphosphate kinase |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: sodium/potassium phosphate, pH pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K PH range: pH 4.5 |
-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: Mar 10, 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: 2.95→104.59 Å / Num. obs: 6148 / % possible obs: 98 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.5 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry: 1NSK Resolution: 2.95→104.59 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.834 / SU B: 18.685 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.417 / 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: 63.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→104.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.025 Å / Total num. of bins used: 20
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