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Yorodumi- PDB-1wxx: Crystal structure of Tt1595, a putative SAM-dependent methyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wxx | ||||||
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Title | Crystal structure of Tt1595, a putative SAM-dependent methyltransferase from Thermus thermophillus HB8 | ||||||
Components | hypothetical protein TTHA1280Hypothesis | ||||||
Keywords | TRANSFERASE / Thermus thermophillus / methyltransferase / Adomet / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information 23S rRNA (cytosine1962-C5)-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / methylation / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pioszak, A.A. / Murayama, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine. Authors: Pioszak, A.A. / Murayama, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wxx.cif.gz | 332.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wxx.ent.gz | 267.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wxx ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wxx | HTTPS FTP |
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-Related structure data
Related structure data | 1wxwSC 2cwwC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | There are two biological dimers in the ASU. |
-Components
#1: Protein | Mass: 43252.895 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SIT4 #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-PO4 / #4: 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: 2.88 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.8M NaK Phosphate, 3% sucrose, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.964 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 328489 / Num. obs: 328489 / % possible obs: 93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 1.45 % / Biso Wilson estimate: 11 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 70.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WXW Resolution: 1.8→39.55 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 474167.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.2738 Å2 / ksol: 0.386466 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→39.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
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Xplor file |
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