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Yorodumi- PDB-5lsm: Crystal structure of nitronate monooxygenase (SO_0471) from Shewa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lsm | ||||||
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Title | Crystal structure of nitronate monooxygenase (SO_0471) from Shewanella oneidensis MR-1 | ||||||
Components | FMN-dependent nitronate monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / NITRONATE MONOXYGENASE / 2-NITROPROPANE | ||||||
Function / homology | Function and homology information nitronate monooxygenase activity / response to toxic substance / nucleotide binding Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Baker, G.E. / Race, P.R. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of nitronate monooxygenase (SO_0471) from Shewanella oneidensis MR-1 Authors: Baker, G.E. / Race, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lsm.cif.gz | 499.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lsm.ent.gz | 404 KB | Display | PDB format |
PDBx/mmJSON format | 5lsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lsm_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 5lsm_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 5lsm_validation.xml.gz | 96.8 KB | Display | |
Data in CIF | 5lsm_validation.cif.gz | 131.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/5lsm ftp://data.pdbj.org/pub/pdb/validation_reports/ls/5lsm | HTTPS FTP |
-Related structure data
Related structure data | 2gjlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38019.324 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria) Strain: MR-1 / Gene: SO_0471 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EJJ2, nitronate monooxygenase #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-GOL / #4: 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: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 M potassium dihydrogen phosphate and 20 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97833 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97833 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→34.16 Å / Num. obs: 99971 / % possible obs: 95 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.343 / CC1/2: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GJL Resolution: 2.5→34.16 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.444 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.554 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.158 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→34.16 Å
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