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Yorodumi- PDB-8sm8: Air-oxidized A. ca TruffO expressed from M9 minimal medium supple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sm8 | ||||||
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Title | Air-oxidized A. ca TruffO expressed from M9 minimal medium supplemented with Fe | ||||||
Components | Putative amidohydrolase | ||||||
Keywords | OXIDOREDUCTASE / oxygenase / amidohydrolase-like / PF04909 | ||||||
Function / homology | 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / carboxy-lyase activity / Amidohydrolase-related / Metal-dependent hydrolase / hydrolase activity / : / Putative amidohydrolase Function and homology information | ||||||
Biological species | Afipia carboxidovorans OM5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Liu, C. / Rittle, J. | ||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2024 Title: Bioinformatic Discovery of a Cambialistic Monooxygenase. Authors: Liu, C. / Powell, M.M. / Rao, G. / Britt, R.D. / Rittle, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sm8.cif.gz | 326.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sm8.ent.gz | 237.9 KB | Display | PDB format |
PDBx/mmJSON format | 8sm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/8sm8 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/8sm8 | HTTPS FTP |
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-Related structure data
Related structure data | 8sm6C 8sm7C 8sm9C 8smaC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43894.559 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Afipia carboxidovorans OM5 (bacteria) / Gene: OCA5_c12850 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6JH23 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.04 Å3/Da / Density % sol: 39.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 4.2M 1,6-Hexanediol, 0.1M BISTRIS, 0.015M MgSO4, 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.74 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74 Å / Relative weight: 1 |
Reflection | Resolution: 2→77.41 Å / Num. obs: 87656 / % possible obs: 91.31 % / Redundancy: 9.1 % / Biso Wilson estimate: 18.72 Å2 / CC1/2: 0.881 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2→2.072 Å / Num. unique obs: 35285 / CC1/2: 0.164 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→77.41 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.265 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→77.41 Å
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Refine LS restraints |
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LS refinement shell |
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