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Yorodumi- PDB-1nsq: MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE:... -
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-Basic information
Entry | Database: PDB / ID: 1nsq | ||||||
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Title | MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase | ||||||
Keywords | PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase ...regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase / nucleotide metabolic process / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / adherens junction organization / nucleoside diphosphate kinase activity / microtubule-based process / mitotic cell cycle / kinase activity / microtubule binding / microtubule / phosphorylation / GTP binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.18 Å | ||||||
Authors | Janin, J. / Chiadmi, M. / Morera, S. / Lebras, G. / Lascu, I. | ||||||
Citation | 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. #1: Journal: Structure / Year: 1993 Title: Crystal Structure of the Awd Nucleoside Diphosphate Kinase from Drosophila Authors: Chiadmi, M. / Morera, S. / Lascu, I. / Dumas, C. / Lebras, G. / 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 | 1nsq.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nsq.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/1nsq ftp://data.pdbj.org/pub/pdb/validation_reports/ns/1nsq | HTTPS FTP |
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-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: 17270.830 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P08879, nucleoside-diphosphate kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.53 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / 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 | Resolution: 2.17→15.1 Å / Num. obs: 32198 / % possible obs: 79 % |
Reflection | *PLUS Num. measured all: 184822 / Rmerge(I) obs: 0.077 |
-Processing
Software |
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Refinement | Resolution: 2.18→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.18→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 31522 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22 Å2 |