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Yorodumi- PDB-4n45: Crystal structure of reduced form of thiolase from Clostridium ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n45 | |||||||||
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Title | Crystal structure of reduced form of thiolase from Clostridium acetobutylicum | |||||||||
Components | Acetyl-CoA acetyltransferase | |||||||||
Keywords | TRANSFERASE / alpha/beta/alpha/beta/alpha domain / Acetyl-coA acetyltransferase | |||||||||
Function / homology | Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | |||||||||
Biological species | Clostridium acetobutylicum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | |||||||||
Authors | Kim, S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Lim, J.H. / Kim, K.J. | |||||||||
Citation | Journal: to be published Title: Structural insight into redox-switch regulatory mechanism of thiolase from the n-butanol synthesizing bacterium, Clostridium acetobutylicum Authors: Kim, S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Lim, J.H. / Son, H.C. / Ryu, Y.S. / Lee, S.K. / 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 | 4n45.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n45.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 4n45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n45_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 4n45_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 4n45_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 4n45_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n45 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n45 | HTTPS FTP |
-Related structure data
Related structure data | 4n44SC 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: 42345.496 Da / Num. of mol.: 2 / Mutation: C378S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: EA 2018 / Gene: CEA_G2880 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: F0K5D8, acetyl-CoA C-acetyltransferase #2: 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: 2.42 Å3/Da / Density % sol: 49.25 % / Mosaicity: 1.397 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: PEG3350, K-citrate, NaCl, pH 4.2, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.23985 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.23985 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 5.6 % / Number: 188962 / Rmerge(I) obs: 0.094 / Χ2: 0.86 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 34028 / % possible obs: 81.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.59→50 Å / Num. obs: 108716 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N44 Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.238 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 81.5 Å2 / Biso mean: 21.3347 Å2 / Biso min: 6.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.595→1.636 Å / Total num. of bins used: 20
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