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Yorodumi- PDB-6ioi: Crystal structure of Homoserine O-acetyltransferase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ioi | ||||||
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Title | Crystal structure of Homoserine O-acetyltransferase in complex with CoA from Mycobacterium smegmatis ATCC 19420 | ||||||
Components | Homoserine O-acetyltransferase | ||||||
Keywords | TRANSFERASE / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information homoserine O-acetyltransferase / homoserine O-acetyltransferase activity / methionine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sagong, H.-Y. / Kim, K.-J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Crystal structure and biochemical characterization of O-acetylhomoserine acetyltransferase from Mycobacterium smegmatis ATCC 19420. Authors: Sagong, H.Y. / Hong, J. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ioi.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ioi.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ioi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/6ioi ftp://data.pdbj.org/pub/pdb/validation_reports/io/6ioi | HTTPS FTP |
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-Related structure data
Related structure data | 6iogSC 6iohC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39475.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: metX_1, metXA, ERS451418_01697 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_T1R(DE3) References: UniProt: A0A0D6HE46, UniProt: A0QSZ0*PLUS, homoserine O-acetyltransferase #2: Chemical | #3: 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: 2.56 Å3/Da / Density % sol: 51.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 34 % (v/v) polyethylene glycol (PEG) 400, 0.1 M Sodium acetate/acetic acid pH 5.5, 0.2 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 24, 2018 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 105196 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 46 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 9.56 / Num. unique obs: 5234 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IOG Resolution: 1.6→30.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.39 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 125.86 Å2 / Biso mean: 16.62 Å2 / Biso min: 8.06 Å2
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Refinement step | Cycle: final / Resolution: 1.6→30.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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