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Yorodumi- PDB-1n71: Crystal structure of aminoglycoside 6'-acetyltransferase type Ii ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n71 | ||||||
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Title | Crystal structure of aminoglycoside 6'-acetyltransferase type Ii in complex with coenzyme A | ||||||
Components | aac(6')-Ii | ||||||
Keywords | TRANSFERASE / AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE / ANTIBIOTIC RESISTANCE / COENZYME A | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Burk, D.L. / Ghuman, N. / Wybenga-Groot, L.E. / Berghuis, A.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: X-ray structure of the AAC(6')-Ii antibiotic resistance enzyme at 1.8 A resolution; examination of oligomeric arrangements in GNAT superfamily members Authors: Burk, D.L. / Ghuman, N. / Wybenga-Groot, L.E. / Berghuis, A.M. #1: Journal: Structure / Year: 1999 Title: Crystal structure of an aminoglycoside 6'-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold Authors: Wybenga-Groot, L.E. / Draker, K. / Wright, G.D. / Berghuis, A.M. | ||||||
History |
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Remark 999 | SEQUENCE The author states that there is an error in the sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n71.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n71.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n71_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1n71_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1n71_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 1n71_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n71 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n71 | HTTPS FTP |
-Related structure data
Related structure data | 1b87S 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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2 |
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3 |
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Unit cell |
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Details | Asymmetric unit contains two biological units (dimers) |
-Components
#1: Protein | Mass: 20514.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Plasmid: pPLaac-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47764 #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 2.02 Å3/Da / Density % sol: 38.54 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.97 Å / Num. all: 64971 / Num. obs: 64971 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 100 Å / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 67.6 % / Redundancy: 3.1 % / Num. unique obs: 4590 / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1B87 with cofactor and water removed Resolution: 1.8→27.97 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / 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: 45.5792 Å2 / ksol: 0.359296 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.203 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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