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Yorodumi- PDB-4b3i: Crystal structure of Mycobacterium tuberculosis fatty acid beta- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b3i | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis fatty acid beta- oxidation complex with CoenzymeA bound at the hydratase active sites | ||||||
Components | (FATTY ACID BETA-OXIDATION COMPLEX ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE/TRANSFERASE / OXIDOREDUCTASE-TRANSFERASE COMPLEX / TFE / TRIFUNCTIONAL ENZYME / HETERO TETRAMER / COA | ||||||
Function / homology | Function and homology information long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid beta-oxidation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.63 Å | ||||||
Authors | Venkatesan, R. / Wierenga, R.K. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Structure of Mycobacterial Beta-Oxidation Trifunctional Enzyme Reveals its Altered Assembly and Putative Substrate Channeling Pathway. Authors: Venkatesan, R. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b3i.cif.gz | 831.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b3i.ent.gz | 692.1 KB | Display | PDB format |
PDBx/mmJSON format | 4b3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b3i ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b3i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-FATTY ACID BETA-OXIDATION COMPLEX ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 78005.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET DUET, PACYC DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS References: UniProt: O53872, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase #2: Protein | Mass: 42460.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET DUET, PACYC DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: O53871, acetyl-CoA C-acetyltransferase |
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-Non-polymers , 5 types, 818 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 3.88 Å3/Da / Density % sol: 68.33 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 2M AMMONIUM SULFATE, 0.1 M TRIS PH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2011 |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→51.07 Å / Num. obs: 103601 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.63→2.77 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.63→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.777 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
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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: 38.784 Å2
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Refinement step | Cycle: LAST / Resolution: 2.63→50 Å
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Refine LS restraints |
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