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Yorodumi- PDB-7o4v: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o4v | ||||||||||||
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Title | Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with oxidized nicotinamide adenine dinucleotide | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / trifunctional enzyme / fatty acid beta oxidation / mycobacterium tuberculosis | ||||||||||||
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 H37Rv (bacteria) Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||||||||
Authors | Dalwani, S. / Wierenga, R.K. / Venkatesan, R. | ||||||||||||
Funding support | Finland, 3items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme. Authors: Dalwani, S. / Lampela, O. / Leprovost, P. / Schmitz, W. / Juffer, A.H. / Wierenga, R.K. / Venkatesan, R. #1: 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 | 7o4v.cif.gz | 1012.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o4v.ent.gz | 707.1 KB | Display | PDB format |
PDBx/mmJSON format | 7o4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/7o4v ftp://data.pdbj.org/pub/pdb/validation_reports/o4/7o4v | HTTPS FTP |
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-Related structure data
Related structure data | 7o1gC 7o1iC 7o1jC 7o1kC 7o1lC 7o1mC 7o4qC 7o4rC 7o4sC 7o4tC 7o4uC 4b3hS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 78005.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: fadB, Rv0860 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O53872, 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 (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: fadA, Rv0859 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.67 Å3/Da / Density % sol: 66.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8.5 / Details: 2M (NH4)2SO4, 100mM Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→86.84 Å / Num. obs: 131141 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.04 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.42→2.46 Å / Num. unique obs: 6486 / CC1/2: 0.289 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B3H Resolution: 2.42→72.92 Å / SU ML: 0.4271 / Cross valid method: FREE R-VALUE / σ(F): 0.78 / Phase error: 30.6396 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→72.92 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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