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Yorodumi- PDB-1y9w: Structural Genomics, 1.9A crystal structure of an acetyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y9w | ||||||
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Title | Structural Genomics, 1.9A crystal structure of an acetyltransferase from Bacillus cereus ATCC 14579 | ||||||
Components | Acetyltransferase | ||||||
Keywords | TRANSFERASE / Bacillus cereus / acetyltransferase / Structural Genomics / Protein Structure Initiative / PSI / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Zhang, R. / Li, H. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published / Year: 2005 Title: 1.9A crystal structure of an acetyltransferase from Bacillus cereus ATCC 14579 Authors: Zhang, R. / Li, H. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y9w.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y9w.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 1y9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y9w_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
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Full document | 1y9w_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 1y9w_validation.xml.gz | 16 KB | Display | |
Data in CIF | 1y9w_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/1y9w ftp://data.pdbj.org/pub/pdb/validation_reports/y9/1y9w | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This protein existed as dimer, the Mol.A and Mol.B represent the dimer in the assymmetric unit. |
-Components
#1: Protein | Mass: 16485.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: gi:29896479 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q81CG1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: 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: 2.506 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05M MgCl2, 0.1M HEPES, 30% PEG MME550, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9797,0.94656 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 18, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→40 Å / Num. all: 49031 / Num. obs: 45795 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 30.4 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.18 / Num. unique all: 4920 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→26.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 293105.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.7761 Å2 / ksol: 0.341872 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→26.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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