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Yorodumi- PDB-1hhq: Role of active site resiude Lys16 in Nucleoside Diphosphate Kinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hhq | ||||||
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Title | Role of active site resiude Lys16 in Nucleoside Diphosphate Kinase | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE / METABOLIC ROLE / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Schneider, B. / Babolat, M. / Xu, Y.W. / Janin, J. / Veron, M. / Deville-Bonne, D. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: Mechanism of Phosphoryl Transfer by Nucleoside Diphosphate Kinase Ph-Dependence and Role of Active Site Lys16 and Tyr56 Residues Authors: Schneider, B. / Babolat, M. / Xu, Y.W. / Janin, J. / Veron, M. / Deville-Bonne, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hhq.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hhq.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hhq_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 1hhq_full_validation.pdf.gz | 426.9 KB | Display | |
Data in XML | 1hhq_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 1hhq_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/1hhq ftp://data.pdbj.org/pub/pdb/validation_reports/hh/1hhq | HTTPS FTP |
-Related structure data
Related structure data | 1npkS S: Starting model for refinement |
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Similar 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: 16758.234 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: AMMOUNIUM SULFATE / Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED MUTATION LYS16ALA PLAYS A MAJOR ROLE IN THE SYNTHESIS OF NUCLEOSIDE ...CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: METHOD: HANGING DROP IN DROP: 5MG/ML PROTEIN, 50 MM TRIS HCL PH7.5, 1 M AS, 20MM MGCL2 IN WELL: 2M AS, 50MM TRISHCL PH7.5, 20MM MGCL2, pH 7.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 11016 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.1 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 98.2 % / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NPK Resolution: 2.1→20 Å / σ(F): 2
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Displacement parameters | Biso mean: 18.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.201 / Rfactor Rfree: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.321 / Rfactor obs: 0.259 |