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- PDB-1el9: COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1el9 | ||||||
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Title | COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE | ||||||
![]() | SARCOSINE OXIDE | ||||||
![]() | 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 | ![]() | ||||||
![]() | Wagner, M.A. / Trickey, P. / Chen, Z.-W. / Mathews, F.S. / Jorns, M.S. | ||||||
![]() | ![]() Title: Monomeric sarcosine oxidase: 1. Flavin reactivity and active site binding determinants. Authors: Wagner, M.A. / Trickey, P. / 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 | ![]() | 173.2 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1el5C ![]() 1el7C ![]() 1el8C ![]() 1eliC ![]() 1b3m C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43429.617 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 , 5 types, 561 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MTG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MTG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.62 % Description: MAD phasing was not used to solve 1EL9 and 1ELI, but rather direct refinement as the crystals were isomorphous enough to the native crystals for phasing. Selenomethionine crystals were ...Description: MAD phasing was not used to solve 1EL9 and 1ELI, but rather direct refinement as the crystals were isomorphous enough to the native crystals for phasing. Selenomethionine crystals were used for the experiments since they were the only ones on hand at the time. Kinetic studies showed that the presence of selenomethionine had little effect. | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: phosphate, tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 8 Details: drop consists of equal amounts of protein and reservoir solutions | ||||||||||||||||||||
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 / Detector: IMAGE PLATE / Date: Jul 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→500 Å / Num. all: 49552 / Num. obs: 43804 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.25 / Num. unique all: 2639 / % possible all: 53.6 |
Reflection shell | *PLUS % possible obs: 53.6 % |
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Processing
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Refinement | Resolution: 2→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→500 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.311 / Rfactor Rwork: 0.278 |