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Yorodumi- PDB-2yxe: Crystal structure of L-isoaspartyl protein carboxyl methyltranferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yxe | ||||||
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Title | Crystal structure of L-isoaspartyl protein carboxyl methyltranferase | ||||||
Components | Protein-L-isoaspartate O-methyltransferase | ||||||
Keywords | TRANSFERASE / Rossman-type fold / alpha/beta/alpha sandwich structure / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information protein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / protein repair / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Padmanabhan, B. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of L-isoaspartyl protein carboxyl methyltranferase Authors: Padmanabhan, B. / Bessho, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yxe.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yxe.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 2yxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yxe_validation.pdf.gz | 380.3 KB | Display | wwPDB validaton report |
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Full document | 2yxe_full_validation.pdf.gz | 385.4 KB | Display | |
Data in XML | 2yxe_validation.xml.gz | 10 KB | Display | |
Data in CIF | 2yxe_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yxe ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yxe | HTTPS FTP |
-Related structure data
Related structure data | 1jg4S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 23791.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Gene: pcm / Plasmid: pET-21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: Q57636, protein-L-isoaspartate(D-aspartate) O-methyltransferase #2: Chemical | #3: 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: 3.29 Å3/Da / Density % sol: 62.61 % |
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Crystal grow | Temperature: 298 K / Method: oil batch / pH: 4.5 Details: 0.1M Acetate, 40% 1,2-propanediol, pH 4.5, Oil batch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD |
Radiation | Monochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 43589 / Num. obs: 42769 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.9 % / Num. unique all: 3629 / Rsym value: 0.24 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JG4 Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.186 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.241 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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