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Yorodumi- PDB-1jg2: Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jg2 | ||||||
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Title | Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine | ||||||
Components | protein-L-isoaspartate O-methyltransferase | ||||||
Keywords | TRANSFERASE / Rossman 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jg2.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jg2.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jg2_validation.pdf.gz | 755.9 KB | Display | wwPDB validaton report |
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Full document | 1jg2_full_validation.pdf.gz | 757.1 KB | Display | |
Data in XML | 1jg2_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1jg2_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jg2 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jg2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-ADN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.07 % | ||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 118 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2000 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→500 Å / Num. all: 30345 / Num. obs: 30345 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.458 / % possible all: 95.3 |
Reflection | *PLUS Lowest resolution: 500 Å / Num. measured all: 119506 |
Reflection shell | *PLUS % possible obs: 97.8 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→500 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.221 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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