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- PDB-6oxc: Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oxc | |||||||||
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Title | Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin | |||||||||
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![]() | 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 | ![]() | 515.9 KB | Display | ![]() |
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PDB format | ![]() | 414.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 59.6 KB | Display | |
Data in CIF | ![]() | 92.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oxdC ![]() 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
#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, 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 |
#3: Chemical | ChemComp-B12 / |
#4: Chemical | ChemComp-5AD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM sodium cacodylate/HCl, pH 6.5, 800 mM sodium citrate tribasic dihydrate, 0.05% w/v casein, 0.05% w/v hemoglobin, 0.0005% w/v pepsin, 0.0005% w/v protease, 0.0005% w/v Proteinase K, 0. ...Details: 100 mM sodium cacodylate/HCl, pH 6.5, 800 mM sodium citrate tribasic dihydrate, 0.05% w/v casein, 0.05% w/v hemoglobin, 0.0005% w/v pepsin, 0.0005% w/v protease, 0.0005% w/v Proteinase K, 0.0005% w/v trypsin, 0.002 M HEPES sodium, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 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: 1.9→29.1 Å / Num. obs: 129672 / % possible obs: 96.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 24.6 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.16 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6274 / CC1/2: 0.636 / Rrim(I) all: 1.104 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2REQ Resolution: 1.9→28.967 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.967 Å
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Refine LS restraints |
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LS refinement shell |
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