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Yorodumi- PDB-3fyd: Crystal Structure of Dim1 from the thermophilic archeon, Methanoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fyd | ||||||
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Title | Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi | ||||||
Components | Probable dimethyladenosine transferase | ||||||
Keywords | TRANSFERASE / dimethyladenosine transferase / rossmann fold / rRNA methylase / ribosomal assembly / Methyltransferase / RNA-binding / rRNA processing / S-adenosyl-L-methionine | ||||||
Function / homology | Function and homology information rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Scarsdale, J.N. / Musayev, F.N. / Rife, J.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. Authors: Pulicherla, N. / Pogorzala, L.A. / Xu, Z. / O Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / Sia, E.A. / Culver, G.M. / Rife, J.P. #1: Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. Authors: O'Farrell, H.C. / Scarsdale, J.N. / Rife, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fyd.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fyd.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fyd ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fyd | HTTPS FTP |
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-Related structure data
Related structure data | 3fycC 1qyrS 1zq9S 2h1rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30316.139 Da / Num. of mol.: 1 / Mutation: K137A, E138A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: ksgA, MJ1029 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q58435, Transferases; Transferring one-carbon groups; Methyltransferases | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 8000 (14-16%), 25 mM MES, 50 MM NH2SO4, 7 mM MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 3, 2008 / Details: Rigaku Varimax Confocal Optics |
Radiation | Monochromator: Rigaku Varimax Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→33.1 Å / Num. all: 31119 / Num. obs: 29365 / % possible obs: 94.4 % / Redundancy: 7.06 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 6.98 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3079 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 Resolution: 1.75→22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.061 / SU ML: 0.087 Isotropic thermal model: TLS for each domain + individual residual isotropic B-factors Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Structure was initially refined with cartesian annealing with phenix.refine followed by refinement with refmac.
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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: 43.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.257 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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