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- PDB-8opy: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8opy | ||||||||||||
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Title | Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-B-DNQ | ||||||||||||
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![]() | OXIDOREDUCTASE / fatty acid beta oxidation complex / mycobacterium tuberculosis / TFE / fragment screening / substrate channeling | ||||||||||||
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: Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them. Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R. #1: ![]() Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate channeling path between them Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R. #2: ![]() Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme. Authors: Dalwani, S. #3: ![]() Title: Structure of mycobacterial beta-oxidation trifunctional enzyme reveals its altered assembly and putative substrate channeling pathway. Authors: 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 | ![]() | 997.5 KB | Display | ![]() |
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PDB format | ![]() | 687.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8opuC ![]() 8opvC ![]() 8opwC ![]() 8opxC ![]() 8oqlC ![]() 8oqmC ![]() 8oqnC ![]() 8oqoC ![]() 8oqpC ![]() 8oqqC ![]() 8oqrC ![]() 8oqsC ![]() 8oquC ![]() 8oqvC ![]() 8pf8C ![]() 4b3hS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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.) ![]() Gene: fadA, Rv0859 / Production host: ![]() ![]() References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 4 types, 158 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DNQ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DNQ.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #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: 3.87 Å3/Da / Density % sol: 68.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / 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: Aug 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.895 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→48.21 Å / Num. obs: 133151 / % possible obs: 98.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.62 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.42 |
Reflection shell | Resolution: 2.45→2.59 Å / Num. unique obs: 20542 / CC1/2: 0.53 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4B3H Resolution: 2.45→47.01 Å / SU ML: 0.4288 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.2486 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: 65.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→47.01 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -43.7590502499 Å / Origin y: 33.8572856645 Å / Origin z: -1.85376420166 Å
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Refinement TLS group | Selection details: all |