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Yorodumi- PDB-1l9c: Role of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l9c | ||||||
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Title | Role of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase | ||||||
Components | Monomeric Sarcosine Oxidase | ||||||
Keywords | OXIDOREDUCTASE / flavoprotein / oxidase | ||||||
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 / refined directly / Resolution: 1.9 Å | ||||||
Authors | Zhao, G. / Song, H. / Chen, Z.-w. / Mathews, F.S. / Jorns, M.S. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Monomeric sarcosine oxidase: role of histidine 269 in catalysis. Authors: Zhao, G. / Song, H. / Chen, Z.W. / Mathews, F.S. / Jorns, M.S. #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 | 1l9c.cif.gz | 191.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l9c.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 1l9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l9c_validation.pdf.gz | 928.9 KB | Display | wwPDB validaton report |
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Full document | 1l9c_full_validation.pdf.gz | 946.6 KB | Display | |
Data in XML | 1l9c_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 1l9c_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/1l9c ftp://data.pdbj.org/pub/pdb/validation_reports/l9/1l9c | HTTPS FTP |
-Related structure data
Related structure data | 1l9dC 1l9eC 1b3m 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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Details | The biological assembly is monomer. |
-Components
#1: Protein | Mass: 43077.312 Da / Num. of mol.: 2 / Mutation: H269N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: B-0618 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #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: 42.4 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP at 295K, temperature 295.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 18, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 57652 / Num. obs: 50561 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3011 / % possible all: 52.5 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.95 Å / % possible obs: 52.5 % / Rmerge(I) obs: 0.192 |
-Processing
Software |
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Refinement | Method to determine structure: refined directly Starting model: PDB code 1B3M 1b3m Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.171 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.95 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.243 |