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Yorodumi- PDB-2a89: Monomeric Sarcosine Oxidase: Structure of a covalently flavinylat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a89 | ||||||
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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 sarcosine oxidase (formaldehyde-forming) / sarcosine oxidase activity / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Chen, Z.-W. / Zhao, G. / Martinovic, S. / Jorns, M.S. / Mathews, F.S. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structure of the sodium borohydride-reduced N-(cyclopropyl)glycine adduct of the flavoenzyme monomeric sarcosine oxidase. Authors: Chen, Z.-W. / Zhao, G. / Martinovic, S. / Jorns, M.S. / Mathews, F.S. #1: Journal: Structure / Year: 1999 Title: Monomeric Sarcosine Oxidase: Structure of a covalently flavinylated amine oxidizing enzyme Authors: Trickey, P. / Wagner, M.A. / Jorn, 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 | 2a89.cif.gz | 191.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a89.ent.gz | 146.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/2a89 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/2a89 | HTTPS FTP |
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-Related structure data
Related structure data | 1l9f 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: 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 | #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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: Na/K phosphate, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-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 IV / Detector: IMAGE PLATE / Date: Jul 7, 2000 |
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: 1.85→40 Å / Num. all: 62473 / Num. obs: 55726 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.85 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3058 / % possible all: 49.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L9F 1l9f Resolution: 1.85→40 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: 16.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→40 Å
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Refine LS restraints |
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LS refinement shell |
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