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Yorodumi- PDB-5byv: Crystal structure of MSM-13, a putative T1-like thiolase from Myc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5byv | ||||||
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Title | Crystal structure of MSM-13, a putative T1-like thiolase from Mycobacterium smegmatis | ||||||
Components | Beta-ketothiolase | ||||||
Keywords | TRANSFERASE / thiolase / mycobacterium smegmatis / T1-like / tetrameric | ||||||
Function / homology | Function and homology information acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / fatty acid beta-oxidation / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å | ||||||
Authors | Janardan, N. / Harijan, R.K. / Keima, T.R. / Wierenga, R. / Murthy, M.R.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis Authors: Janardan, N. / Harijan, R.K. / Kiema, T.R. / Wierenga, R.K. / 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 | 5byv.cif.gz | 874.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5byv.ent.gz | 730.2 KB | Display | PDB format |
PDBx/mmJSON format | 5byv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5byv_validation.pdf.gz | 512.6 KB | Display | wwPDB validaton report |
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Full document | 5byv_full_validation.pdf.gz | 560.7 KB | Display | |
Data in XML | 5byv_validation.xml.gz | 169.9 KB | Display | |
Data in CIF | 5byv_validation.cif.gz | 237 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5byv ftp://data.pdbj.org/pub/pdb/validation_reports/by/5byv | HTTPS FTP |
-Related structure data
Related structure data | 4zrcC 5bz4C 5cbqC 4zecS 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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Unit cell |
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-Components
#1: Protein | Mass: 43007.824 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: MC2 155 / Gene: MSMEG_2207 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QUH3 #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: 2.7 Å3/Da / Density % sol: 54.43 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6 Details: 45% PEG 200, 0.1M MES monohydrate pH 6.0, 0.07M calcium chloride dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→45.193 Å / Num. obs: 290242 / % possible obs: 99.94 % / Redundancy: 1.9 % / Net I/σ(I): 12.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZEC Resolution: 2.162→45.193 Å / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 24.35 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.162→45.193 Å
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Refine LS restraints |
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LS refinement shell |
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