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- PDB-2gf3: Structure of the complex of monomeric sarcosine with its substrat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gf3 | ||||||
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Title | Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution. | ||||||
![]() | Monomeric sarcosine oxidase | ||||||
![]() | OXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / INHIBITOR 2-FUROIC ACID | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Chen, Z. / Trickey, P. / Jorns, M.S. / Mathews, F.S. | ||||||
![]() | ![]() Title: Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 A resolution. Authors: Chen, Z. / Trickey, P. / Jorns, M.S. / Mathews, F.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 | ![]() | 193.6 KB | Display | ![]() |
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PDB format | ![]() | 149.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 973.6 KB | Display | ![]() |
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Full document | ![]() | 989.3 KB | Display | |
Data in XML | ![]() | 41.8 KB | Display | |
Data in CIF | ![]() | 64 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1l9f 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 a monomer. |
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Components
-Protein , 1 types, 2 molecules AB
#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) |
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-Non-polymers , 6 types, 1005 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FOA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FOA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FOA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 1.8-2.1M Sodium/potassium phosphate, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 178944 / Num. obs: 170534 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20 |
Reflection shell | Highest resolution: 1.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 1.9 / % possible all: 82.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L9F ![]() 1l9f Resolution: 1.3→14.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1532946.36 / Data cutoff low absF: 0 / 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: 17.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→14.98 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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