[English] 日本語
Yorodumi- PDB-1jg1: Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jg1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with S-ADENOSYL-L-HOMOCYSTEINE | ||||||
Components | protein-L-isoaspartate O-methyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann methyltransferase / PROTEIN REPAIR ISOMERIZATION | ||||||
Function / homology | Function and homology information protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / protein repair / protein modification process / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å | ||||||
Authors | Griffith, S.C. / Sawaya, M.R. / Boutz, D. / Thapar, N. / Katz, J. / Clarke, S. / Yeates, T.O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate. Authors: Griffith, S.C. / Sawaya, M.R. / Boutz, D.R. / Thapar, N. / Katz, J.E. / Clarke, S. / Yeates, T.O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jg1.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jg1.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jg1_validation.pdf.gz | 705 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jg1_full_validation.pdf.gz | 706 KB | Display | |
Data in XML | 1jg1_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1jg1_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jg1 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jg1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26613.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) References: UniProt: Q8TZR3, protein-L-isoaspartate(D-aspartate) O-methyltransferase |
---|---|
#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.08 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG 2000, 15% Glycerol, 0.2 M Ammonium Acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 118 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2000 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→500 Å / Num. all: 61904 / Num. obs: 61904 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.385 / % possible all: 97.7 |
Reflection | *PLUS Lowest resolution: 500 Å / % possible obs: 97.7 % / Num. measured all: 427037 |
Reflection shell | *PLUS % possible obs: 86.6 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.2→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→500 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.15 / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.147 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|