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Yorodumi- PDB-3qse: Crystal structure for the complex of substrate-reduced msox with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qse | ||||||
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Title | Crystal structure for the complex of substrate-reduced msox with sarcosine | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Kommoju, P. / Chen, Z. / Bruckner, R.C. / Mathews, F.S. / Jorns, M.S. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate. Authors: Kommoju, P.R. / Chen, Z.W. / Bruckner, R.C. / 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 | 3qse.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qse.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 3qse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/3qse ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qse | HTTPS FTP |
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-Related structure data
Related structure data | 3qsmC 3qssC 3qvpC 3qvrC 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: 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 | #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: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M Na/K phosphate, 120 MM sarcosine, then soaked with 2.3 M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING 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: Dec 22, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: APS Beamline 14-BM-C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→40 Å / Num. all: 71893 / Num. obs: 70527 / % possible obs: 98.1 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 4.6 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1L9F 1l9f Resolution: 1.75→25.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 268939.76 / 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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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.8423 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→25.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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