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Yorodumi- PDB-8jg2: Crystal structure of a biosynthetic thiolase from Megasphaera hex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jg2 | ||||||
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Title | Crystal structure of a biosynthetic thiolase from Megasphaera hexanoica soaked with hexanoyl-CoA | ||||||
Components | Acetyl-CoA C-acetyltransferase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / acetyl-coenzyme A C-acyltransferase | ||||||
Function / homology | Function and homology information acetyl-CoA C-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Megasphaera hexanoica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Kim, E.-J. / Seo, H. / Kim, K.-J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of biosynthetic thiolase from Megasphaera hexanoica Authors: Jeon, B.S. / Kim, E.-J. / Kim, K.-J. / Sang, B.-I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jg2.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jg2.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jg2_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8jg2_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8jg2_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 8jg2_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/8jg2 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jg2 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 46091.727 Da / Num. of mol.: 2 / Mutation: C88S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Megasphaera hexanoica (bacteria) / Gene: HF872_02440 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A848BQU5 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.22 Å3/Da / Density % sol: 44.67 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25 % w/v polyethylene glycol (PEG) 3350 and 0.1M HEPES pH 7.5 |
-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: 0.97935 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 3, 2016 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→38.99 Å / Num. obs: 99877 / % possible obs: 99.61 % / Redundancy: 2 % / Biso Wilson estimate: 21.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02374 / Rpim(I) all: 0.02374 / Rrim(I) all: 0.03357 / Net I/σ(I): 12.08 |
Reflection shell | Resolution: 1.64→1.699 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2768 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 9827 / CC1/2: 0.853 / CC star: 0.96 / Rpim(I) all: 0.2768 / Rrim(I) all: 0.3915 / % possible all: 99.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→38.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.965 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.103 / 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: 22.664 Å2
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Refinement step | Cycle: 1 / Resolution: 1.64→38.99 Å
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