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Yorodumi- PDB-1ndc: X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ndc | |||||||||
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Title | X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION | |||||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | |||||||||
Keywords | PHOSPHOTRANSFERASE / NUCLEOSIDE TRIPHOSPHATE / NUCLEOSIDE DIPHOSPHATE | |||||||||
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 / CTP 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 / CTP biosynthetic process / UTP 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 / Resolution: 2 Å | |||||||||
Authors | Cherfils, J. / Morera, S. / Janin, J. | |||||||||
Citation | Journal: Biochemistry / Year: 1994 Title: X-ray structure of nucleoside diphosphate kinase complexed with thymidine diphosphate and Mg2+ at 2-A resolution. Authors: Cherfils, J. / Morera, S. / Lascu, I. / Veron, M. / Janin, J. #1: Journal: Biochemistry / Year: 1994 Title: Adp Binding and the Active Site of Nucleoside Diphosphate Kinase Authors: Morera, S. / Lascu, I. / Dumas, C. / Lebras, G. / Briozzo, P. / 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 | 1ndc.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ndc.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ndc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ndc_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 1ndc_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 1ndc_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1ndc_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndc ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndc | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16816.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / References: UniProt: P22887, nucleoside-diphosphate kinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-TYD / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | A MG++ ION IS ASSOCIATED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 16 Å / Num. obs: 13562 / % possible obs: 99.6 % / Num. measured all: 71549 / Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Resolution: 2→16 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2→16 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 13562 / Rfactor all: 0.183 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.6 |