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Yorodumi- PDB-1el7: COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1el7 | |||||||||
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Title | COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYTELLURO]ACETATE | |||||||||
Components | SARCOSINE OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / flavoprotein / oxidase | |||||||||
Function / homology | Function and homology information 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 | Bacillus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | |||||||||
Authors | Wagner, M.A. / Trickey, P. / Chen, Z.-W. / Mathews, F.S. / Jorns, M.S. | |||||||||
Citation | Journal: Biochemistry / Year: 2000 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: 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 | 1el7.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1el7.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 1el7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/1el7 ftp://data.pdbj.org/pub/pdb/validation_reports/el/1el7 | HTTPS FTP |
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-Related structure data
Related structure data | 1el5C 1el8C 1el9C 1eliC 1b3m C: citing same article (ref.) |
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Similar structure data |
-Links
-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. |
-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.) Bacillus sp. (bacteria) / Strain: B-0618 / Cell (production host): DH1 CELLS / Production host: Escherichia coli (E. coli) References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming) |
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-Non-polymers , 6 types, 810 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.72 % | ||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 11, 1999 |
Radiation | 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→500 Å / Num. all: 56174 / Num. obs: 52916 / % possible obs: 94.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.248 / Num. unique all: 2481 / % possible all: 62.3 |
Reflection shell | *PLUS % possible obs: 62.3 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Resolution: 1.9→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.9→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 |