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Yorodumi- PDB-1ncl: THERMAL STABILITY OF HEXAMERIC AND TETRAMERIC NUCLEOSIDE, DIPHOSP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ncl | ||||||
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Title | THERMAL STABILITY OF HEXAMERIC AND TETRAMERIC NUCLEOSIDE, DIPHOSPHATE KINASES | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / ENZYME / KINASE / ATP-BINDING | ||||||
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 / phosphorylation / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Janin, J. / Morera, S. / Lascu, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: Thermal stability of hexameric and tetrameric nucleoside diphosphate kinases. Effect of subunit interaction. Authors: Giartosio, A. / Erent, M. / Cervoni, L. / Morera, S. / Janin, J. / Konrad, M. / Lascu, I. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Refined X-Ray Structure of Dictyostelium Discoideum Nucleoside Diphosphate Kinase at 1.8 A Resolution Authors: Morera, S. / Lebras, G. / Lascu, I. / Lacombe, M.L. / Veron, M. / Janin, J. #2: Journal: Embo J. / Year: 1992 Title: X-Ray Structure of Nucleoside Diphosphate Kinase Authors: Dumas, C. / Lascu, I. / Morera, S. / Glaser, P. / Fourme, R. / Wallet, V. / Lacombe, M.L. / Veron, M. / Janin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ncl.cif.gz | 41.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ncl.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ncl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1ncl ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1ncl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16213.608 Da / Num. of mol.: 1 / Mutation: P105G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.91 |
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Detector | Type: MARRESEARCH / Date: May 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Redundancy: 2.6 % / Rmerge(I) obs: 0.063 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 8556 / % possible obs: 93 % / Num. measured all: 22178 |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |