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Yorodumi- PDB-1j7i: Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j7i | ||||||
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Title | Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa Apoenzyme | ||||||
Components | AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE | ||||||
Keywords | TRANSFERASE / antibiotic resistance / kinase / ATP-binding | ||||||
Function / homology | Function and homology information kanamycin kinase / kanamycin kinase activity / response to antibiotic / ATP binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Burk, D.L. / Hon, W.C. / Leung, A.K.-W. / Berghuis, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase. Authors: Burk, D.L. / Hon, W.C. / Leung, A.K. / Berghuis, A.M. #1: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Structure of an Enzyme Required for Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases Authors: Hon, W.C. / McKay, G.A. / Thompson, P.R. / Sweet, R.M. / Yang, D.S. / Wright, G.D. / Berghuis, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j7i.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j7i.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j7i_validation.pdf.gz | 364.8 KB | Display | wwPDB validaton report |
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Full document | 1j7i_full_validation.pdf.gz | 371.3 KB | Display | |
Data in XML | 1j7i_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1j7i_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j7i ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j7i | 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: 31012.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pPCRG6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A3Y5, kanamycin kinase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, magnesium chloride, ammonium sulfate, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 5165 / Num. obs: 5165 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.3 / % possible all: 96.7 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 15937 |
Reflection shell | *PLUS Highest resolution: 3.2 Å / % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→35.6 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 73178.08 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 128.9 Å2 / ksol: 0.3476 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→35.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.219 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.337 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.271 |