+Open data
-Basic information
Entry | Database: PDB / ID: 1kdn | ||||||
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Title | STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / TRANSFERASE / 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 / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Cherfils, J. / Xu, Y.W. / Morera, S. / Janin, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Authors: Xu, Y.W. / Morera, S. / Janin, J. / Cherfils, J. #1: Journal: Biochemistry / Year: 1995 Title: Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium Authors: Morera, S. / Chiadmi, M. / Lebras, G. / Lascu, I. / Janin, J. #2: Journal: Biochemistry / Year: 1994 Title: Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase Authors: Morera, S. / Lascu, I. / Dumas, C. / Lebras, G. / Briozzo, P. / 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 | 1kdn.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kdn.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kdn_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1kdn_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1kdn_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 1kdn_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/1kdn ftp://data.pdbj.org/pub/pdb/validation_reports/kd/1kdn | HTTPS FTP |
-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: 16816.336 Da / Num. of mol.: 3 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 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
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 / Beamline: DW32 / Wavelength: 0.906 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.906 Å / Relative weight: 1 |
Reflection | Num. obs: 30088 / % possible obs: 96.3 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 118259 |
-Processing
Software |
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Refinement | Highest resolution: 2 Å / σ(F): 2
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Displacement parameters | Biso mean: 18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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