+Open data
-Basic information
Entry | Database: PDB / ID: 1nd4 | ||||||
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Title | Crystal structure of aminoglycoside-3'-phosphotransferase-IIa | ||||||
Components | Aminoglycoside 3'-phosphotransferase | ||||||
Keywords | TRANSFERASE / phosphotransferase / protein kinase / ATPase / kanamycin | ||||||
Function / homology | Function and homology information kanamycin kinase / kanamycin kinase activity / response to antibiotic / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nurizzo, D. / Shewry, S.C. / Baker, E.N. / Smith, C.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The crystal structure of aminoglycoside-3'-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance Authors: Nurizzo, D. / Shewry, S.C. / Perlin, M.H. / Brown, S.A. / Dholakia, J.N. / Fuchs, R.L. / Deva, T. / Baker, E.N. / Smith, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nd4.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nd4.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1nd4 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1nd4 | HTTPS FTP |
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-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29078.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00552, kanamycin kinase |
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-Non-polymers , 5 types, 373 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.93 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 100mM cacodylate, 150mM magnesium acetate, 20-26% PEG8000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 4.5 Å / % possible obs: 99.4 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 99.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→34 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 34 Å | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS |