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Yorodumi- PDB-2qhs: Structural Basis of Octanoic Acid Recognition by Lipoate-Protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qhs | ||||||
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Title | Structural Basis of Octanoic Acid Recognition by Lipoate-Protein Ligase B | ||||||
Components | Lipoyltransferase | ||||||
Keywords | TRANSFERASE / globular protein | ||||||
Function / homology | Function and homology information lipoyl(octanoyl) transferase / lipoyl(octanoyl) transferase activity / organic substance biosynthetic process / cellular biosynthetic process / protein modification process / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Kim, D.J. / Lee, S.J. / Kim, H.S. / Kim, K.H. / Lee, H.H. / Yoon, H.J. / Suh, S.W. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structural basis of octanoic acid recognition by lipoate-protein ligase B Authors: Kim, D.J. / Lee, S.J. / Kim, H.S. / Kim, K.H. / Lee, H.H. / Yoon, H.J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qhs.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qhs.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/2qhs ftp://data.pdbj.org/pub/pdb/validation_reports/qh/2qhs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26123.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTC 1746 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) pLysS References: UniProt: Q5SLQ3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Chemical | ChemComp-OCA / |
#3: 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: 2.21 Å3/Da / Density % sol: 44.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50mM HEPES at pH 7.0, 4.0M lithium chloride, 5%(v/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97925, 0.97942, 0.95000 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→20 Å / Num. obs: 38216 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.1 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.951 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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