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Yorodumi- PDB-4n44: Crystal structure of oxidized form of thiolase from Clostridium a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n44 | ||||||
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Title | Crystal structure of oxidized 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 / ACETATE ION / : Function and homology information | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 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 | 4n44.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n44.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 4n44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n44 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n44 | HTTPS FTP |
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-Related structure data
Related structure data | 4n45C 1dlvS 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: 42361.559 Da / Num. of mol.: 2 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: Chemical | ChemComp-ACT / #3: Chemical | #4: 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: 0.493 ° |
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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: Oct 17, 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: 5.3 % / Number: 410057 / Rmerge(I) obs: 0.07 / Χ2: 1.76 / D res high: 1.77 Å / D res low: 50 Å / Num. obs: 77934 / % possible obs: 98.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.77→50 Å / Num. all: 79061 / Num. obs: 77934 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.063 / Net I/σ(I): 33.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1DLV Resolution: 1.77→43.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.299 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.11 / 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: 141.27 Å2 / Biso mean: 30.7619 Å2 / Biso min: 13.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→43.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.818 Å / Total num. of bins used: 20
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