+Open data
-Basic information
Entry | Database: PDB / ID: 6ak1 | ||||||
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Title | Crystal structure of DmoA from Hyphomicrobium sulfonivorans | ||||||
Components | Dimethyl-sulfide monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Dimethylsulfide monooxygenase / TIM barrel | ||||||
Function / homology | Function and homology information dissimilatory dimethyl sulfide monooxygenase / dimethyl sulfide monooxygenase activity Similarity search - Function | ||||||
Biological species | Hyphomicrobium sulfonivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.284 Å | ||||||
Authors | Cao, H.Y. / Wang, P. / Peng, M. / Li, C.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2018 Title: Crystal structure of the dimethylsulfide monooxygenase DmoA from Hyphomicrobium sulfonivorans. Authors: Cao, H.Y. / Wang, P. / Peng, M. / Shao, X. / Chen, X.L. / Li, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ak1.cif.gz | 200.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ak1.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ak1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ak1_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 6ak1_full_validation.pdf.gz | 433.8 KB | Display | |
Data in XML | 6ak1_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 6ak1_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6ak1 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6ak1 | HTTPS FTP |
-Related structure data
Related structure data | 3b9oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54248.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphomicrobium sulfonivorans (bacteria) Gene: dmoA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: E9JFX9, dissimilatory dimethyl sulfide monooxygenase #2: 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: 2.51 Å3/Da / Density % sol: 50.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris propane, PEG 3350, sodium iodide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 47759 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.28→2.38 Å / Rmerge(I) obs: 0.279 / Num. unique obs: 4320 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B9O Resolution: 2.284→49.215 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.284→49.215 Å
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Refine LS restraints |
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LS refinement shell |
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