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Yorodumi- PDB-7o4u: Structure of the alpha subunit of Mycobacterium tuberculosis beta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o4u | ||||||||||||
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Title | Structure of the alpha subunit of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with oxidized nicotinamide adenine dinucleotide | ||||||||||||
Components | 3-hydroxyacyl-CoA dehydrogenase | ||||||||||||
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 / fatty acid beta-oxidation / NAD+ binding / peptidoglycan-based cell wall / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 7o4u.cif.gz | 648 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o4u.ent.gz | 449.2 KB | Display | PDB format |
PDBx/mmJSON format | 7o4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/7o4u ftp://data.pdbj.org/pub/pdb/validation_reports/o4/7o4u | HTTPS FTP |
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-Related structure data
Related structure data | 7o1gC 7o1iC 7o1jC 7o1kC 7o1lC 7o1mC 7o4qC 7o4rC 7o4sC 7o4tC 7o4vC 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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2 |
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Unit cell |
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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: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.3 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 22% PEG 4000, 0.1 M TEA pH 7.5, 20% IPA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→88.9 Å / Num. obs: 38685 / % possible obs: 97.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 59.37 Å2 / CC1/2: 0.988 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.7→2.82 Å / Num. unique obs: 4735 / CC1/2: 0.867 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B3H Resolution: 2.7→88.9 Å / SU ML: 0.4947 / Cross valid method: FREE R-VALUE / σ(F): 0.72 / Phase error: 30.8834 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: 71.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→88.9 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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