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- PDB-1r18: Drosophila protein isoaspartyl methyltransferase with S-adenosyl-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r18 | ||||||
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Title | Drosophila protein isoaspartyl methyltransferase with S-adenosyl-L-homocysteine | ||||||
![]() | Protein-L-isoaspartate(D-aspartate)-O-methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase / isomerization / protein repair / S-adenosyl homocysteine | ||||||
Function / homology | ![]() Protein repair / protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / defense response to bacterium / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bennett, E.J. / Bjerregaard, J. / Knapp, J.E. / Chavous, D.A. / Friedman, A.M. / Royer Jr., W.E. / O'Connor, C.M. | ||||||
![]() | ![]() Title: Catalytic implications from the Drosophila protein L-isoaspartyl methyltransferase structure and site-directed mutagenesis. Authors: Bennett, E.J. / Bjerregaard, J. / Knapp, J.E. / Chavous, D.A. / Friedman, A.M. / Royer Jr., W.E. / O'Connor, C.M. #1: ![]() Title: Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6A resolution and modeling of an isoaspartyl-containing peptide at the active site Authors: Smith, C.D. / Carson, M. / Friedman, A.M. / Skinner, M.M. / Delucas, L. / Chantalat, L. / Weise, L. / Shirasawa, T. / Chattopadhyay, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.7 KB | Display | ![]() |
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PDB format | ![]() | 39.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 712.4 KB | Display | ![]() |
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Full document | ![]() | 715.2 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i1nS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24597.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q27869, protein-L-isoaspartate(D-aspartate) O-methyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.79 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM Tris, 35% v/v Ethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2002 / Details: osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 8636 / Num. obs: 8636 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.232 / Num. unique all: 761 / Rsym value: 0.232 / % possible all: 79.6 |
Reflection | *PLUS % possible obs: 89 % / Num. measured all: 14628 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 79.6 % / Num. unique obs: 761 / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Human PIMT (pdb code 1I1N) Resolution: 2.2→20.97 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.122 Å2 / ksol: 0.318386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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