+Open data
-Basic information
Entry | Database: PDB / ID: 3n4u | ||||||
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Title | app APH(2")-IVa form II | ||||||
Components | APH(2'')-Id | ||||||
Keywords | UNKNOWN FUNCTION / aminoglycoside / phosphotransferase / resistance | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus casseliflavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Smith, C.A. / Toth, M. / Frase, H. / Vakulenko, S.B. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Crystal structure and kinetic mechanism of aminoglycoside phosphotransferase-2''-IVa. Authors: Toth, M. / Frase, H. / Antunes, N.T. / Smith, C.A. / Vakulenko, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n4u.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n4u.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 3n4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n4u ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n4u | 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: 35425.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / References: UniProt: O68183 |
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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: 1.98 Å3/Da / Density % sol: 37.77 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28.61 Å / Num. all: 16313 / Num. obs: 16313 / % possible obs: 96 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.3 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.61 Å / SU ML: 0.32 / σ(F): 1.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.727 Å2 / ksol: 0.282 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.61 Å
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Refine LS restraints |
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LS refinement shell |
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