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Yorodumi- PDB-6n93: Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n93 | ||||||
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Title | Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-oxa(dethia)-CoA | ||||||
Components | Methylmalonyl-CoA decarboxylase | ||||||
Keywords | LYASE / crotonase / beta-keto / isostere | ||||||
Function / homology | Function and homology information methyl/ethyl malonyl-CoA decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / fatty acid beta-oxidation / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Stunkard, L.M. / Dixon, A.D. / Huth, T.J. / Lohman, J.R. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2019 Title: Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies. Authors: Stunkard, L.M. / Dixon, A.D. / Huth, T.J. / Lohman, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n93.cif.gz | 385.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n93.ent.gz | 311.8 KB | Display | PDB format |
PDBx/mmJSON format | 6n93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n93_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 6n93_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 6n93_validation.xml.gz | 85 KB | Display | |
Data in CIF | 6n93_validation.cif.gz | 124.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/6n93 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n93 | HTTPS FTP |
-Related structure data
Related structure data | 6n92SC 6n94C 6n95C 6n96C 6n97C S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 29190.557 Da / Num. of mol.: 6 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: scpB, mmcD, ygfG, b2919, JW2886 / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P52045, Lyases; Carbon-carbon lyases; Carboxy-lyases |
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-Non-polymers , 7 types, 1983 molecules
#2: Chemical | ChemComp-KGA / [ #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-KG7 / ( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 150 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate, 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2016 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 203268 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Rsym value: 0.11 / Χ2: 0.888 / Net I/av σ(I): 14.375 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.192 / Mean I/σ(I) obs: 1.167 / Num. unique obs: 10028 / Rsym value: 1.192 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N92 Resolution: 1.7→28.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Matrix type: sparse / SU B: 2.178 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1004 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.098 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.25 Å2 / Biso mean: 16.898 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 1.7→28.68 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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