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- PDB-7o4r: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o4r | ||||||||||||
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Title | Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme with Coenzyme A bound at the thiolase active sites and additional binding site (CoA(HAD/KAT)) | ||||||||||||
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![]() | OXIDOREDUCTASE / trifunctional enzyme / fatty acid beta oxidation / mycobacterium tuberculosis | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Dalwani, S. / Wierenga, R.K. / Venkatesan, R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 532.4 KB | Display | ![]() |
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PDB format | ![]() | 351.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
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Full document | ![]() | 502.5 KB | Display | |
Data in XML | ![]() | 41.2 KB | Display | |
Data in CIF | ![]() | 63.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o1gC ![]() 7o1iC ![]() 7o1jC ![]() 7o1kC ![]() 7o1lC ![]() 7o1mC ![]() 7o4qC ![]() 7o4sC ![]() 7o4tC ![]() 7o4uC ![]() 7o4vC ![]() 4b3hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 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.) ![]() Gene: fadB, Rv0860 / Production host: ![]() ![]() 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.) ![]() Strain: ATCC 25618 / H37Rv / Gene: fadA, Rv0859 / Production host: ![]() ![]() References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 4 types, 259 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-COA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8.5 / Details: 2 M Ammonium Sulfate, 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→48.5 Å / Num. obs: 81071 / % possible obs: 95.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.68 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.79→2.9 Å / Num. unique obs: 4054 / CC1/2: 0.473 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4B3H Resolution: 2.79→48.5 Å / SU ML: 0.3365 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.8104 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: 49.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→48.5 Å
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Refine LS restraints |
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LS refinement shell |
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