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- PDB-6oxd: Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oxd | |||||||||
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Title | Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin | |||||||||
![]() | (Methylmalonyl-CoA mutase ...) x 2 | |||||||||
![]() | ISOMERASE / methylmalonyl CoA mutase / methylmalonyl CoA mutase deficiency / metabolic disease / cobalamin / cobalt / disease mutation / metal-binding / itaconyl CoA / radical / Mycobacterium tuberculosis / immunometabolite / B12 / methylmalonic aciduria | |||||||||
Function / homology | ![]() lactate fermentation to propionate and acetate / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / cobalamin binding / peptidoglycan-based cell wall / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Purchal, M. / Ruetz, M. / Banerjee, R. / Koutmos, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair. Authors: Ruetz, M. / Campanello, G.C. / Purchal, M. / Shen, H. / McDevitt, L. / Gouda, H. / Wakabayashi, S. / Zhu, J. / Rubin, E.J. / Warncke, K. / Mootha, V.K. / Koutmos, M. / Banerjee, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 512.4 KB | Display | ![]() |
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PDB format | ![]() | 412.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.8 KB | Display | ![]() |
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Full document | ![]() | 486.3 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oxcC ![]() 2reqS C: citing same article ( S: Starting model for refinement |
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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
-Methylmalonyl-CoA mutase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 80692.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mutB, DK316_08225, DSI35_00620, ERS027651_01113, ERS027652_00280, ERS124361_00189, SAMEA2682864_01878, SAMEA2683035_01024 Production host: ![]() ![]() References: UniProt: A0A0E8UW09, UniProt: P9WJK5*PLUS, methylmalonyl-CoA mutase |
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#2: Protein | Mass: 64869.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mutA, DK316_08220, ERS007663_02000, ERS023446_02236, ERS027651_01114, ERS027656_01366, ERS124361_00188, SAMEA2682864_01877, SAMEA2683035_01025 Production host: ![]() ![]() References: UniProt: A0A045IZR3, UniProt: P9WJK7*PLUS, methylmalonyl-CoA mutase |
-Non-polymers , 5 types, 1124 molecules ![](data/chem/img/B12.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/NJS.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/NJS.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-B12 / |
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#4: Chemical | ChemComp-5AD / |
#5: Chemical | ChemComp-NJS / |
#6: Chemical | ChemComp-K / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.4 M sodium phosphate monobasic, 1.6 M potassium phosphate dibasic, 0.1 M imidazole/HCl, pH 8, 0.2 M sodium chloride |
-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 7, 2018 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.8 Å / Num. obs: 104126 / % possible obs: 98.4 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.127 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.997 / Num. unique obs: 5172 / CC1/2: 0.622 / Rrim(I) all: 1.243 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2REQ Resolution: 2→29.798 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.798 Å
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Refine LS restraints |
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LS refinement shell |
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