[English] 日本語
![](img/lk-miru.gif)
- PDB-3bhk: Crystal structure of R49K mutant of monomeric sarcosine oxidase c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3bhk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of R49K mutant of monomeric sarcosine oxidase crystallized in phosphate as precipitant | ||||||
![]() | MONOMERIC SARCOSINE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / FAD | ||||||
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 | ![]() ![]() | ||||||
![]() | Hassan-Abdallah, A. / Zhao, G. / Chen, Z. / Mathews, F.S. / Jorns, M.S. | ||||||
![]() | ![]() Title: Arginine 49 is a bifunctional residue important in catalysis and biosynthesis of monomeric sarcosine oxidase: a context-sensitive model for the electrostatic impact of arginine to lysine mutations. Authors: Hassan-Abdallah, A. / Zhao, G. / Chen, Z.W. / Mathews, F.S. / Schuman Jorns, M. #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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 180.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 936.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 953.6 KB | Display | |
Data in XML | ![]() | 38.3 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bhfC ![]() 1l9f C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43204.535 Da / Num. of mol.: 2 / Mutation: R49K 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.62 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8 M Na/K phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 78950 / Num. obs: 74292 / % possible obs: 94.1 % / Observed criterion σ(F): -0.6 / Observed criterion σ(I): -0.6 / Redundancy: 3.3 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6441 / % possible all: 82.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Refined directly Starting model: PDB entry 1L9F ![]() 1l9f Resolution: 1.71→32.4 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 386700.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→32.4 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.71→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
|