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Yorodumi- PDB-2gb0: Monomeric sarcosine oxidase: structure of a covalently flavinylat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gb0 | |||||||||
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Title | Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme | |||||||||
Components | Monomeric sarcosine oxidase | |||||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN OXIDASE | |||||||||
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. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.85 Å | |||||||||
Authors | Trickey, P. / Wagner, M.A. / Jorns, M.S. / Mathews, F.S. | |||||||||
Citation | 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 | 2gb0.cif.gz | 177.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gb0.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 2gb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/2gb0 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/2gb0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 43101.355 Da / Num. of mol.: 2 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 | ChemComp-PO4 / #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: 2.16 Å3/Da / Density % sol: 43.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: PHOSPHATE, VAPOR DIFFUSION, SITTING DROP AT 298K, pH 6.70 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 0.9792, 0.9794, 0.9392, 1.0679 | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 8, 1998 | |||||||||||||||
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→43 Å / Num. all: 62740 / Num. obs: 58976 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.6 | |||||||||||||||
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.5 / % possible all: 57.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→42.53 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 947266.85 / Data cutoff low absF: 0 / 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: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→42.53 Å
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Refine LS restraints |
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LS refinement shell |
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