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Yorodumi- PDB-2yr0: Crystal Structure of Hypothetical Methyltransferase TTHA0223 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yr0 | ||||||
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Title | Crystal Structure of Hypothetical Methyltransferase TTHA0223 from Thermus thermophilus HB8 | ||||||
Components | Hypothetical protein TTHA0223Hypothesis | ||||||
Keywords | TRANSFERASE / RNA methyltransferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kagawa, W. / Kurumizaka, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Crystal Structure of Hypothetical Methyltransferase TTHA0223 from Thermus thermophilus HB8 Authors: Kagawa, W. / Kurumizaka, H. / Yokoyama, S. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ...BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. DETAILS: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yr0.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yr0.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/2yr0 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/2yr0 | HTTPS FTP |
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-Related structure data
Related structure data | 2yqzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29874.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q5SLS0, Transferases; Transferring one-carbon groups; Methyltransferases #2: 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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 0.2M CaCl2, 20%(w/v) PEG 3350, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9792, 0.9000, 0.9797 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 9, 2006 | ||||||||||||
Radiation | Monochromator: SI DOUBLE-CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 39396 / Num. obs: 37923 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3838 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2YQZ Resolution: 1.9→41.37 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→41.37 Å
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Refine LS restraints |
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LS refinement shell |
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