+Open data
-Basic information
Entry | Database: PDB / ID: 3qsm | ||||||
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Title | Crystal structure for the MSOX.chloride binary complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 3qsm.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qsm.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 3qsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/3qsm ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qsm | HTTPS FTP |
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-Related structure data
Related structure data | 3qseC 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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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 | ChemComp-CL / #4: 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: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M Na/K phosphate. Then the crystal was soaked with 2.5 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 29, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Yale mirrors / 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→40 Å / Num. all: 55769 / Num. obs: 54598 / % possible obs: 97.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.8 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.9→32.24 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 172335.21 / 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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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→32.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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