+Open data
-Basic information
Entry | Database: PDB / ID: 1b87 | ||||||
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Title | CRYSTAL STRUCTURE OF AN AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE | ||||||
Components | PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1) | ||||||
Keywords | TRANSFERASE / AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE / ANTIBIOTIC RESISTANCE / ACETYL 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 / MAD / Resolution: 2.7 Å | ||||||
Authors | Wybenga-Groot, L.E. / Berghuis, A.M. | ||||||
Citation | Journal: Structure Fold.Des. / 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b87.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b87.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 1b87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b87_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 1b87_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 1b87_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1b87_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b87 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b87 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20602.066 Da / Num. of mol.: 1 / Mutation: VAL127GLU / Source method: isolated from a natural source / Source: (natural) Enterococcus faecium (bacteria) / References: UniProt: Q47764 |
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#2: Chemical | ChemComp-ACO / |
#3: 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: 3.2 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9809, 0.9795, 0.9792, 0.9770 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 1998 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→40 Å / Num. obs: 6085 / % possible obs: 89.7 % / Redundancy: 2.1 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 12.7 / Net I/σ(I): 4.3 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.94 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Rsym value: 33.2 / % possible all: 88.9 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.127 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 88.9 % / Rmerge(I) obs: 0.332 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→40 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 11.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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