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Yorodumi- PDB-1ej0: FTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE, M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ej0 | ||||||
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Title | FTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE, MERCURY DERIVATIVE | ||||||
Components | FTSJ | ||||||
Keywords | TRANSFERASE / ftsj / methyltransferase / adomet / adenosyl methionine / heat shock proteins / 23S RIBOSOMAL RNA | ||||||
Function / homology | Function and homology information 23S rRNA (uridine2552-2'-O)-methyltransferase / rRNA (uridine-2'-O-)-methyltransferase activity / RNA methylation / rRNA processing / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Bugl, H. / Fauman, E.B. / Staker, B.L. / Zheng, F. / Kushner, S.R. / Saper, M.A. / Bardwell, J.C.A. / Jakob, U. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: RNA methylation under heat shock control. Authors: Bugl, H. / Fauman, E.B. / Staker, B.L. / Zheng, F. / Kushner, S.R. / Saper, M.A. / Bardwell, J.C. / Jakob, U. #1: Journal: J.Biol.Chem. / Year: 2000 Title: The FtsJ/RrmJ heat shock protein of escherichia coli is a 23 S ribosomal RNA methyltransferase. Authors: Caldas, T. / Binet, E. / Bouloc, P. / Costa, A. / Desgres, J. / Richarme, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ej0.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ej0.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ej0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ej0_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 1ej0_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 1ej0_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1ej0_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ej0 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ej0 | HTTPS FTP |
-Related structure data
Related structure data | 1eizSC 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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 19937.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P28692, UniProt: P0C0R7*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | #3: Chemical | ChemComp-SAM / | #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: 2.2 Å3/Da / Density % sol: 44.07 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.65 Details: 1mM Adomet, 33% PEG 4000, 0.19 ammonium acetate, 0.1 M sodium citrate pH 5.65, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 54471 / Num. obs: 51445 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.38 / % possible all: 62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EIZ Resolution: 1.5→17.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 87999367.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used bulk solvent correction. Used anomalous data.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.77 Å2 / ksol: 0.44 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→17.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.367 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.345 |