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Yorodumi- PDB-3g8w: Crystal structure of a probable acetyltransferase from Staphyloco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g8w | ||||||
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Title | Crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228 | ||||||
Components | Lactococcal prophage ps3 protein 05 | ||||||
Keywords | TRANSFERASE / APC61042 / acetyltransferase / Staphylococcus epidermidis ATCC 12228 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus epidermidis ATCC 12228 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Tan, K. / Sather, A. / Marshall, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a probable acetyltransferase from Staphylococcus epidermidis ATCC 12228. Authors: Tan, K. / Sather, A. / Marshall, N. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g8w.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g8w.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 3g8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/3g8w ftp://data.pdbj.org/pub/pdb/validation_reports/g8/3g8w | HTTPS FTP |
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-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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2 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN. IT IS LIKELY A DIMER WITH THE ASSEMBLY SHOWN IN REMARK 350. |
-Components
#1: Protein | Mass: 19975.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis ATCC 12228 (bacteria) Gene: SE_0588 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8CPX3, UniProt: A0A0H2VFJ4*PLUS #2: Chemical | ChemComp-NHE / #3: Chemical | ChemComp-FLC / | #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: 3.69 Å3/Da / Density % sol: 66.69 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1M CHES, 1.0M Sodium citrate, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97940 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2008 / Details: mirror | |||||||||
Radiation | Monochromator: Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. all: 32550 / Num. obs: 32550 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 37.8 | |||||||||
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1598 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→49.39 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 23.19 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.46 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Monomer D is partially disordered.
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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: 44.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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