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- PDB-7o4t: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o4t | ||||||||||||
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Title | Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme with Coenzyme A bound at the hydratase, thiolase active sites and possible additional binding site (CoA(ECH/HAD)) | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 548 KB | Display | ![]() |
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PDB format | ![]() | 358.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7o1gC ![]() 7o1iC ![]() 7o1jC ![]() 7o1kC ![]() 7o1lC ![]() 7o1mC ![]() 7o4qC ![]() 7o4rC ![]() 7o4sC ![]() 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, ![]() #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, ![]() |
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-Non-polymers , 5 types, 303 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PAP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PAP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-COA / ![]() #4: Chemical | ![]() #5: Chemical | #6: Chemical | ChemComp-SO4 / ![]() #7: 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: 68.29 % |
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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: Nov 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→58.74 Å / Num. obs: 212119 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 51.73 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 10533 / CC1/2: 0.41 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4B3H Resolution: 2.1→58.74 Å / SU ML: 0.3477 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 31.0567 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: 66.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→58.74 Å
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Refine LS restraints |
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LS refinement shell |
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