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Yorodumi- PDB-1wy7: crystal structure of a putative RNA methyltransferase PH1948 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wy7 | ||||||
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Title | crystal structure of a putative RNA methyltransferase PH1948 from Pyrococcus horikoshii | ||||||
Components | hypothetical protein PH1948Hypothesis | ||||||
Keywords | TRANSFERASE / seven-stranded beta sheet / methyltransferase fold / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Gao, Y.G. / Yao, M. / Tanaka, I. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of the putative RNA methyltransferase PH1948 from Pyrococcus horikoshii, in complex with the copurified S-adenosyl-L-homocysteine Authors: Gao, Y.G. / Yao, M. / Yong, Z. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wy7.cif.gz | 171.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wy7.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/1wy7 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/1wy7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 23780.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1948 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834-DE3 References: UniProt: O59611, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-SAH / #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: 2.8 Å3/Da / Density % sol: 55.629986 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG400, HEPES-Na, CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.86 Å / Num. all: 53514 / Num. obs: 53514 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 47.46 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.6 / Num. unique all: 5050 / Rsym value: 0.218 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Throughout / Bsol: 54.88 Å2 / ksol: 35.04 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.11 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: ncs restraints for main chain / Weight Biso : 0.3 / Weight position: 200 | |||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.28 Å
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