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- PDB-1l9d: Role of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l9d | ||||||
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Title | Role of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Zhao, G. / Song, H. / Chen, Z.-w. / Mathews, F.S. / Jorns, M.S. | ||||||
![]() | ![]() Title: Monomeric sarcosine oxidase: role of histidine 269 in catalysis. Authors: Zhao, G. / Song, H. / Chen, Z.W. / 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 | ![]() | 141.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 939.6 KB | Display | ![]() |
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Full document | ![]() | 959.3 KB | Display | |
Data in XML | ![]() | 39.4 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1l9cC ![]() 1l9eC ![]() 1b3m 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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Details | The biological assembly is monomer |
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Components
#1: Protein | Mass: 43077.312 Da / Num. of mol.: 2 / Mutation: H269N 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: 2.11 Å3/Da / Density % sol: 41.8 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP at 295K, temperature 295.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 2, 2001 |
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: 1.95→30 Å / Num. all: 52603 / Num. obs: 47553 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2650 / % possible all: 50.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Lowest resolution: 2 Å / % possible obs: 50.8 % / Rmerge(I) obs: 0.25 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code 1B3M ![]() 1b3m Resolution: 1.95→30 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: 23.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.184 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2 Å / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.254 |