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- PDB-3qse: Crystal structure for the complex of substrate-reduced msox with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qse | ||||||
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Title | Crystal structure for the complex of substrate-reduced msox with sarcosine | ||||||
![]() | Monomeric sarcosine oxidase | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN / OXIDASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kommoju, P. / Chen, Z. / Bruckner, R.C. / Mathews, F.S. / Jorns, M.S. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.9 KB | Display | ![]() |
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PDB format | ![]() | 141.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 940.3 KB | Display | ![]() |
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Full document | ![]() | 956.6 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qsmC ![]() 3qssC ![]() 3qvpC ![]() 3qvrC ![]() 1l9f C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]() 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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