+Open data
-Basic information
Entry | Database: PDB / ID: 3slf | ||||||
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Title | Crystal structure of BA2930 in complex with AcCoA and uracil | ||||||
Components | Aminoglycoside N3-acetyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / acetyltransferase | ||||||
Function / homology | Function and homology information aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Klimecka, M.M. / Chruszcz, M. / Porebski, P.J. / Cymborowski, M. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of BA2930 in complex with AcCoA and uracil Authors: Klimecka, M.M. / Chruszcz, M. / Porebski, P.J. / Cymborowski, M. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3slf.cif.gz | 197.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3slf.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 3slf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/3slf ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3slf | HTTPS FTP |
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-Related structure data
Related structure data | 3ijwS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 1 - 264 / Label seq-ID: 4 - 267
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-Components
#1: Protein | Mass: 30337.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: aacC7, BA_2930, GBAA2930, GBAA_2930 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) References: UniProt: Q81P86, UniProt: A0A3P1UCA6*PLUS, aminoglycoside 3-N-acetyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 17% w/v PEG3350, 0.1M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 19, 2010 / Details: beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 34755 / Num. obs: 34755 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.555 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3IJW Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.31 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.499 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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