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Yorodumi- PDB-4zrc: Crystal structure of MSM-13, a putative T1-like thiolase from Myc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zrc | ||||||
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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 / Resolution: 2.7 Å | ||||||
Authors | Janardan, N. / Harijan, R.K. / Keima, T.R. / Wierenga, R. / Murthy, M.R.N. | ||||||
Funding support | India, 1items
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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 | 4zrc.cif.gz | 293.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zrc.ent.gz | 236.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zrc_validation.pdf.gz | 464.4 KB | Display | wwPDB validaton report |
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Full document | 4zrc_full_validation.pdf.gz | 491.7 KB | Display | |
Data in XML | 4zrc_validation.xml.gz | 55.9 KB | Display | |
Data in CIF | 4zrc_validation.cif.gz | 76.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/4zrc ftp://data.pdbj.org/pub/pdb/validation_reports/zr/4zrc | HTTPS FTP |
-Related 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: 1 / Ens-ID: 1 / Refine code: 1
NCS oper:
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-Components
#1: Protein | Mass: 43836.699 Da / Num. of mol.: 4 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: 2.23 Å3/Da / Density % sol: 44.95 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 0.2M sodium acetate trihydrate, 0.1M sodium cacodylatetrihydrate pH 6.5, 30% PEG 8000, 5% n-octyl-D-glucoside |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→47.52 Å / Num. all: 201832 / Num. obs: 201832 / % possible obs: 98.92 % / Redundancy: 1 % / Net I/σ(I): 8.2 |
-Processing
Software |
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Refinement | Resolution: 2.7→47.52 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.843 / SU B: 16.328 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 44.306 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→47.52 Å
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Refine LS restraints |
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