+Open data
-Basic information
Entry | Database: PDB / ID: 1leo | ||||||
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Title | P100S NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / ENZYME / 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 / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / negative regulation of phagocytosis / 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: 2.6 Å | ||||||
Authors | Janin, J. / Xu, Y. / Veron, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography. Authors: Karlsson, A. / Mesnildrey, S. / Xu, Y. / Morera, S. / Janin, J. / Veron, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1leo.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1leo.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1leo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1leo ftp://data.pdbj.org/pub/pdb/validation_reports/le/1leo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16243.634 Da / Num. of mol.: 1 / Mutation: P100S 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: 2.63 Å3/Da / Density % sol: 53.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / 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: 1.375 |
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Detector | Type: MARRESEARCH / Date: Jun 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Num. obs: 5623 / % possible obs: 95.6 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.109 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 5263 / Num. measured all: 88483 |
-Processing
Software |
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Refinement | Resolution: 2.6→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.6→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 |