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Yorodumi- PDB-1hlw: STRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hlw | ||||||
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Title | STRUCTURE OF THE H122A MUTANT OF THE NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE / PHOSPHOTRANSFERASE / 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 / Resolution: 1.9 Å | ||||||
Authors | Admiraal, S.J. / Meyer, P. / Schneider, B. / Deville-Bonne, D. / Janin, J. / Herschlag, D. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Chemical rescue of phosphoryl transfer in a cavity mutant: a cautionary tale for site-directed mutagenesis. Authors: Admiraal, S.J. / Meyer, P. / Schneider, B. / Deville-Bonne, D. / Janin, J. / Herschlag, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hlw.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hlw.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hlw_validation.pdf.gz | 362.7 KB | Display | wwPDB validaton report |
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Full document | 1hlw_full_validation.pdf.gz | 362.4 KB | Display | |
Data in XML | 1hlw_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1hlw_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/1hlw ftp://data.pdbj.org/pub/pdb/validation_reports/hl/1hlw | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is a homohexamer |
-Components
#1: Protein | Mass: 16749.268 Da / Num. of mol.: 1 / Mutation: H122A 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 600, Magnesium Chloride, Tris Hydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 110350 / Num. obs: 13910 / % possible obs: 95.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.9→2.02 Å / % possible all: 88 |
Reflection | *PLUS Num. measured all: 110350 |
-Processing
Software |
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Refinement | Resolution: 1.9→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2300066.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.57 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.25 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.214 |