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Yorodumi- PDB-3bhk: Crystal structure of R49K mutant of monomeric sarcosine oxidase c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bhk | ||||||
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Title | Crystal structure of R49K mutant of monomeric sarcosine oxidase crystallized in phosphate as precipitant | ||||||
Components | MONOMERIC SARCOSINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / FAD | ||||||
Function / homology | Function and homology information sarcosine oxidase (formaldehyde-forming) / L-lysine catabolic process to acetyl-CoA via L-pipecolate / L-pipecolate oxidase activity / saccharopine oxidase activity / sarcosine oxidase activity / peroxisome / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Refined directly / Resolution: 1.71 Å | ||||||
Authors | Hassan-Abdallah, A. / Zhao, G. / Chen, Z. / Mathews, F.S. / Jorns, M.S. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Arginine 49 is a bifunctional residue important in catalysis and biosynthesis of monomeric sarcosine oxidase: a context-sensitive model for the electrostatic impact of arginine to lysine mutations. Authors: Hassan-Abdallah, A. / Zhao, G. / Chen, Z.W. / Mathews, F.S. / Schuman Jorns, M. #1: Journal: Structure / Year: 1999 Title: Monomeric Sarcosine Oxidase: Structure of a Covalently Flavinylated Amine Oxidizing Enzyme Authors: Trickey, P. / Wagner, M.A. / Jorns, M.S. / 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 | 3bhk.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bhk.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bhk_validation.pdf.gz | 936.7 KB | Display | wwPDB validaton report |
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Full document | 3bhk_full_validation.pdf.gz | 953.6 KB | Display | |
Data in XML | 3bhk_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 3bhk_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/3bhk ftp://data.pdbj.org/pub/pdb/validation_reports/bh/3bhk | HTTPS FTP |
-Related structure data
Related structure data | 3bhfC 1l9f C: citing same article (ref.) S: Starting model for refinement |
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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: 43204.535 Da / Num. of mol.: 2 / Mutation: R49K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: B-0618 / Gene: soxA, sox / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming) #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.14 Å3/Da / Density % sol: 42.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8 M Na/K phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-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 / Date: Apr 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 78950 / Num. obs: 74292 / % possible obs: 94.1 % / Observed criterion σ(F): -0.6 / Observed criterion σ(I): -0.6 / Redundancy: 3.3 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6441 / % possible all: 82.2 |
-Processing
Software |
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Refinement | Method to determine structure: Refined directly Starting model: PDB entry 1L9F 1l9f Resolution: 1.71→32.4 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 386700.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.71→32.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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