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Yorodumi- PDB-8dyl: Crystal structure of human methylmalonyl-CoA mutase bound to aquo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dyl | |||||||||
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Title | Crystal structure of human methylmalonyl-CoA mutase bound to aquocobalamin | |||||||||
Components | Methylmalonyl-CoA mutase, mitochondrial | |||||||||
Keywords | ISOMERASE / cobalamin / mutase / vitamin B12 | |||||||||
Function / homology | Function and homology information succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process ...succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process / cobalamin binding / post-embryonic development / positive regulation of GTPase activity / mitochondrial matrix / GTPase activity / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Mascarenhas, R.N. / Gouda, H. / Banerjee, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair. Authors: Gouda, H. / Mascarenhas, R. / Ruetz, M. / Yaw, M. / Banerjee, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dyl.cif.gz | 290.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dyl.ent.gz | 229.7 KB | Display | PDB format |
PDBx/mmJSON format | 8dyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dyl_validation.pdf.gz | 773 KB | Display | wwPDB validaton report |
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Full document | 8dyl_full_validation.pdf.gz | 779.2 KB | Display | |
Data in XML | 8dyl_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 8dyl_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/8dyl ftp://data.pdbj.org/pub/pdb/validation_reports/dy/8dyl | HTTPS FTP |
-Related structure data
Related structure data | 8dyjC 2xijS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 84835.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMUT, MUT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22033, methylmalonyl-CoA mutase | ||||
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#2: Chemical | ChemComp-B12 / | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, pH 5.5, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.8 Å / Num. obs: 61448 / % possible obs: 98.4 % / Redundancy: 8.3 % / CC1/2: 1 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique obs: 3258 / CC1/2: 0.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XIJ Resolution: 1.9→39.763 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.55 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.58 Å2 / Biso mean: 36.6386 Å2 / Biso min: 18.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→39.763 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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