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Yorodumi- PDB-1jg3: Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jg3 | ||||||
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Title | Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate | ||||||
Components |
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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 / : / organic substance biosynthetic process / protein repair / cellular biosynthetic process / protein modification process / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 1jg3.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jg3.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jg3 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jg3 | HTTPS FTP |
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-Related 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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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 26613.090 Da / Num. of mol.: 2 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: Protein/peptide | Mass: 701.747 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: hexapeptide substrate |
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-Non-polymers , 4 types, 216 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 50% MPD, 100mM Tris-HCl, 200mM ammonium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 118 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2001 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→500 Å / Num. all: 39722 / Num. obs: 39722 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.435 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 500 Å / Num. measured all: 235211 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→500 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 500 Å / σ(F): 0 / Rfactor obs: 0.211 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |