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Yorodumi- PDB-5uos: Crystal Structure of CblC (MMACHC) (1-238), a human B12 processin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uos | ||||||
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Title | Crystal Structure of CblC (MMACHC) (1-238), a human B12 processing enzyme, complexed with an Antivitamin B12 | ||||||
Components | Methylmalonic aciduria and homocystinuria type C protein | ||||||
Keywords | OXIDOREDUCTASE / Vitamin B12 / B12 trafficking / B12 processing / B12 binding | ||||||
Function / homology | Function and homology information cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / cobalamin metabolic process / Cobalamin (Cbl) metabolism / demethylation / demethylase activity / glutathione binding ...cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / cobalamin metabolic process / Cobalamin (Cbl) metabolism / demethylation / demethylase activity / glutathione binding / cobalamin binding / glutathione metabolic process / FAD binding / transferase activity / oxidoreductase activity / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Shanmuganathan, A. / Karasik, A. / Ruetz, M. / Banerjee, R. / Krautler, B. / Koutmos, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Antivitamin B12 Inhibition of the Human B12 -Processing Enzyme CblC: Crystal Structure of an Inactive Ternary Complex with Glutathione as the Cosubstrate. Authors: Ruetz, M. / Shanmuganathan, A. / Gherasim, C. / Karasik, A. / Salchner, R. / Kieninger, C. / Wurst, K. / Banerjee, R. / Koutmos, M. / Krautler, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uos.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uos.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 5uos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uos_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5uos_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5uos_validation.xml.gz | 13 KB | Display | |
Data in CIF | 5uos_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/5uos ftp://data.pdbj.org/pub/pdb/validation_reports/uo/5uos | HTTPS FTP |
-Related structure data
Related structure data | 3sc0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Monomer confirmed by gel filtration |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27489.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMACHC / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y4U1, Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 7 types, 82 molecules
#2: Chemical | ChemComp-B12 / | ||||
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#3: Chemical | ChemComp-8FS / | ||||
#4: Chemical | ChemComp-GSH / | ||||
#5: Chemical | ChemComp-171 / | ||||
#6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.25 Å3/Da / Density % sol: 76.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.2 M NaCl, 0.1 M CHES:NaOH pH 9.5, 1.26 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2016 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→99.1 Å / Num. obs: 17391 / % possible obs: 86.3 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rsym value: 0.098 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.51→2.62 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1967 / CC1/2: 0.853 / Rpim(I) all: 0.198 / Rsym value: 0.721 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SC0 Resolution: 2.51→99.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.713 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.619 Å2
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Refinement step | Cycle: 1 / Resolution: 2.51→99.1 Å
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