+Open data
-Basic information
Entry | Database: PDB / ID: 3prv | ||||||
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Title | Nucleoside diphosphate kinase B from Trypanosoma cruzi | ||||||
Components | Nucleoside diphosphate kinaseNucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / nucleoside diphosphate kinase b / trypanosomatids / alpha-beta-alpha fold / secreted | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Souza, T.A.C.B. / Trindade, D.M. / Tonoli, C.C.C. / Santos, C.R. / 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 | 3prv.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3prv.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 3prv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/3prv ftp://data.pdbj.org/pub/pdb/validation_reports/pr/3prv | 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: 17571.055 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener Gene: nucleoside diphosphate kinase B GI: 71667531, Tc00.1047053508707.200 Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): delta SlyD / References: UniProt: Q4E256, nucleoside-diphosphate kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 12% (w/v) PEG-3350, 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: 1.4586 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Monochromator: Si (111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→29.4 Å / Num. obs: 28446 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→29.4 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.833 / SU B: 15.76 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / 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: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.238 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→29.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.76 Å / Total num. of bins used: 20
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