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Yorodumi- PDB-4qlo: Crystal Structure of homoserine o-acetyltransferase from Staphylo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qlo | ||||||
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Title | Crystal Structure of homoserine o-acetyltransferase from Staphylococcus aureus | ||||||
Components | homoserine O-acetyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann Fold / Acetyltransferase / AcetylCo-A Binding | ||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å | ||||||
Authors | Thangavelu, B. / Pavlovsky, A.G. / Viola, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Structure of homoserine O-acetyltransferase from Staphylococcus aureus: the first Gram-positive ortholog structure. Authors: Thangavelu, B. / Pavlovsky, A.G. / Viola, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qlo.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qlo.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/4qlo ftp://data.pdbj.org/pub/pdb/validation_reports/ql/4qlo | HTTPS FTP |
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-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: 41244.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: TCH1516 / Gene: AZ30_00060, metX, SACOL0012, USA300HOU_0012 / Plasmid: pDEST42 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8YYT5, homoserine O-acetyltransferase |
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#2: 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: 2.04 Å3/Da / Density % sol: 39.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.7 M Ammonium formate, 100 mM Imidazole hydrochloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2014 Details: HORIZONTALLY AND VERTICALLY FOCUSING BIMORPH MIRRORS IN KIRKPATRICK-BAEZ CONFIGURATION |
Radiation | Monochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 83432 / Num. obs: 12887 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.153 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.646 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.853 / ESU R Free: 0.352 / 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: 57.875 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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