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Yorodumi- PDB-4xl2: Crystal structure of oxidized form of thiolase from Clostridium a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xl2 | ||||||
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Title | Crystal structure of oxidized form of thiolase from Clostridium acetobutylicum | ||||||
Components | Acetyl-CoA acetyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / 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: Nat Commun / Year: 2015 Title: Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum Authors: Kim, S. / Jang, Y.S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Hong Lim, J. / Cho, C. / Shin Ryu, Y. / Kuk Lee, S. / Lee, S.Y. / 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 | 4xl2.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xl2.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xl2_validation.pdf.gz | 484 KB | Display | wwPDB validaton report |
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Full document | 4xl2_full_validation.pdf.gz | 494.7 KB | Display | |
Data in XML | 4xl2_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 4xl2_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/4xl2 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/4xl2 | HTTPS FTP |
-Related structure data
Related structure data | 4wyrC 4wysC 4xl3C 4xl4C 1dlvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 42361.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (bacteria) Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Gene: thlA, thl, CA_C2873 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P45359, acetyl-CoA C-acetyltransferase #2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | #5: 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: 49.11 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: PEG 3350, K-citrate, NaCl |
-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 | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23985 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 79061 / % possible obs: 98.1 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.8 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DLV Resolution: 1.77→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.564 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / 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: 32.174 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→50 Å
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