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Yorodumi- PDB-6sf0: Crystal Structure of Ancestral Flavin-containing monooxygenase (F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sf0 | ||||||
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Title | Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 2 in the presence of NADP+ | ||||||
Components | Ancestral Flavin-containing monooxygenase (FMO) 2 | ||||||
Keywords | OXIDOREDUCTASE / Flavin / enzyme / membrane protein / Ancestral Sequence Reconstruction | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Nicoll, C. / Bailleul, G. / Fiorentini, F. / Mascotti, M.L. / Fraaije, M. / Mattevi, A. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2020 Title: Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs. Authors: Nicoll, C.R. / Bailleul, G. / Fiorentini, F. / Mascotti, M.L. / Fraaije, M.W. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sf0.cif.gz | 441.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sf0.ent.gz | 361.7 KB | Display | PDB format |
PDBx/mmJSON format | 6sf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/6sf0 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/6sf0 | HTTPS FTP |
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-Related structure data
Related structure data | 6se3C 6sekC 6semC 5nmwS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 61169.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Residues 119 - 122 have been omitted from the crystal structure because the electron density around these residues is extremely weak. Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-MA4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.25 Å3/Da / Density % sol: 62.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.01→138 Å / Num. obs: 32052 / % possible obs: 92.4 % / Redundancy: 3.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.145 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.01→3.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2290 / CC1/2: 0.628 / % possible all: 64.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5nmw Resolution: 3.01→138 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 97 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→138 Å
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