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Yorodumi- PDB-3gry: Crystal Structure of the complex between S-Adenosyl Methionine an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gry | ||||||
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Title | Crystal Structure of the complex between S-Adenosyl Methionine and Methanocaldococcus jannaschi Dim1. | ||||||
Components | Dimethyladenosine transferase | ||||||
Keywords | TRANSFERASE / DimethylAdenosine Transferase / Rossmann fold / Ribosomal Assembly S-Adenosyl-L-Methionine / RRNA Processing / RNA-Binding / Methyl Transferase / Methyltransferase / 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: 2.2 Å | ||||||
Authors | Scarsdale, J.N. / Musayev, F.N. / Rife, J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design. Authors: O'Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / 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 | 3gry.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gry.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/3gry ftp://data.pdbj.org/pub/pdb/validation_reports/gr/3gry | HTTPS FTP |
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-Related structure data
Related structure data | 3grrC 3gruC 3grvC 3fydS 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: 33877.305 Da / Num. of mol.: 1 / Mutation: K137A,E138A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: Dim1, 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-SAM / |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.37 Å3/Da / Density % sol: 48.06 % |
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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: Nov 24, 2008 / Details: Rigaku Varimax Confocal Optics |
Radiation | Monochromator: rigkau 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: 2.2→22.34 Å / Num. all: 16190 / Num. obs: 14252 / % possible obs: 88 % / Redundancy: 6.18 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.07 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3 / Num. unique all: 1625 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FYD, Chain A Resolution: 2.2→22.18 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 17.737 / SU ML: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: Residual individual Isotropic B factors with TLS refinement Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.392 Å2
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Refine analyze | Luzzati coordinate error obs: 0.362 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→22.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 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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