+Open data
-Basic information
Entry | Database: PDB / ID: 1hiy | ||||||
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Title | Binding of nucleotides to NDP kinase | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE / METABOLIC ROLE / KINASE | ||||||
Function / homology | Function and homology information dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Cervoni, L. / Lascu, I. / Xu, Y. / Gonin, P. / Morr, M. / Merouani, M. / Janin, J. / Giartoso, A. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Binding of Nucleotides to Nucleoside Diphosphate Kinase: A Calorimetric Study. Authors: Cervoni, L. / Lascu, I. / Xu, Y. / Gonin, P. / Morr, M. / Merouani, M. / Janin, J. / Giartosio, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hiy.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hiy.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/1hiy ftp://data.pdbj.org/pub/pdb/validation_reports/hi/1hiy | HTTPS FTP |
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-Related structure data
Related structure data | 1kdnS 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: 16816.336 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: 3'AMINO-ADP / Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | PLAYS A MAJOR ROLE IN THE SYNTHESIS OF NUCLEOSIDE | |
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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: 2.26 Å3/Da / Density % sol: 31 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: METHOD: HANGING DROP IN DROP: 5MG/ML PROTEIN, 50 MM TRIS HCL PH8.5, 8.5MM 3'-AMINO-ADP,15-16% PEG550, 20MM MGCL2 IN WELL: 30-32% PEG550, 50MM TRISHCL PH8.5., pH 8.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 / Wavelength: 0.97 Å |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 23760 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.049 |
Reflection | *PLUS Lowest resolution: 15 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KDN Resolution: 2.6→15 Å / σ(F): 2
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Displacement parameters | Biso mean: 30.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: BACKBOND RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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