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Yorodumi- PDB-5f0v: X-ray crystal structure of a thiolase from Escherichia coli at 1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f0v | ||||||
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Title | X-ray crystal structure of a thiolase from Escherichia coli at 1.8 A resolution | ||||||
Components | Acetyl-CoA acetyltransferase | ||||||
Keywords | TRANSFERASE / E.coli thiolase / fatty acid metabolism / degradative enzyme / active site geometry | ||||||
Function / homology | Function and homology information acetoacetic acid catabolic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ithayaraja, M. / Neelanjana, J. / Wierenga, R. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystal structure of a thiolase from Escherichia coli at 1.8 angstrom resolution. Authors: Ithayaraja, M. / Janardan, N. / Wierenga, R.K. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f0v.cif.gz | 583.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f0v.ent.gz | 481.9 KB | Display | PDB format |
PDBx/mmJSON format | 5f0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f0v_validation.pdf.gz | 493.9 KB | Display | wwPDB validaton report |
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Full document | 5f0v_full_validation.pdf.gz | 510.4 KB | Display | |
Data in XML | 5f0v_validation.xml.gz | 70.2 KB | Display | |
Data in CIF | 5f0v_validation.cif.gz | 101 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0v ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0v | HTTPS FTP |
-Related structure data
Related structure data | 5f38C 4e1lS 5f0y 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: -1 - 393 / Label seq-ID: 1 - 395
NCS ensembles :
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-Components
#1: Protein | Mass: 40461.434 Da / Num. of mol.: 4 / Fragment: UNP residues 1-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: atoB, b2224, JW2218 / Production host: Escherichia coli (E. coli) / References: UniProt: P76461, acetyl-CoA C-acetyltransferase #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: 0.2 M Ammonium fluride 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.6 Å / Num. obs: 135774 / % possible obs: 99 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E1L Resolution: 1.8→35.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.571 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / 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: 28.293 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→35.6 Å
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Refine LS restraints |
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