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Yorodumi- PDB-2as0: Crystal Structure of PH1915 (APC 5817): A Hypothetical RNA Methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2as0 | ||||||
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Title | Crystal Structure of PH1915 (APC 5817): A Hypothetical RNA Methyltransferase | ||||||
Components | hypothetical protein PH1915Hypothesis | ||||||
Keywords | TRANSFERASE / RNA methyltransferase / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Sun, W. / Xu, X. / Pavlova, M. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Christendat, D. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii. Authors: Sun, W. / Xu, X. / Pavlova, M. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Christendat, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2as0.cif.gz | 170.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2as0.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 2as0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/2as0 ftp://data.pdbj.org/pub/pdb/validation_reports/as/2as0 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45332.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1915 / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O59578, 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: 2.24 Å3/Da / Density % sol: 44.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.2 Details: 1.6 M Ammonium Sulfate, 16 % Glycerol, 0.1 M Sodium Acetate, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 142280 / Num. obs: 142280 / Observed criterion σ(F): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.083 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.521 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→28.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 569200.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.087 Å2 / ksol: 0.387463 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→28.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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