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Yorodumi- PDB-3m12: Crystal Structure of the Lys265Arg phosphate-crytsallized mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m12 | ||||||
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Title | Crystal Structure of the Lys265Arg phosphate-crytsallized mutant of monomeric sarcosine oxidase | ||||||
Components | Monomeric Sarcosine Oxidase | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / FAD / Cytoplasm / Flavoprotein | ||||||
Function / homology | Function and homology information L-lysine catabolic process to acetyl-CoA via L-pipecolate / L-pipecolate oxidase activity / sarcosine oxidase (formaldehyde-forming) / saccharopine oxidase activity / sarcosine oxidase activity / peroxisome / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus sp. b-0618 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / direct refinement from wild type coordinates / Resolution: 1.6 Å | ||||||
Authors | Mathews, F.S. / Chen, Z.-W. / Jorns, M.S. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase. Authors: Jorns, M.S. / Chen, Z.W. / Mathews, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m12.cif.gz | 316.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m12.ent.gz | 256.8 KB | Display | PDB format |
PDBx/mmJSON format | 3m12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/3m12 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/3m12 | HTTPS FTP |
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-Related 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: 43129.371 Da / Num. of mol.: 2 / Mutation: K265R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. b-0618 (bacteria) / Strain: B-0618 / Gene: soxA, sox / Production host: Escherichia coli (E. coli) References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming) #2: Chemical | #3: Chemical | #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: 2.12 Å3/Da / Density % sol: 42.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 1.7 M Na/K phosphate buffer, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 93847 / % possible obs: 99.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.9 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: direct refinement from wild type coordinates Resolution: 1.6→28.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.637 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.63 Å2 / Biso mean: 20.024 Å2 / Biso min: 3.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.602→1.643 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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