+Open data
-Basic information
Entry | Database: PDB / ID: 1gz0 | ||||||
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Title | 23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB | ||||||
Components | HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / 2'O-METHYLTRANSFERASE / KNOT / MONTREAL- KINGSTON BACTERIAL STRUCTURAL GENOMICS INITIATIVE / BSGI / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information 23S rRNA (guanosine2251-2'-O)-methyltransferase / : / rRNA (guanosine-2'-O-)-methyltransferase activity / RNA methyltransferase activity / RNA methylation / RNA binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Michel, G. / Cygler, M. | ||||||
Citation | Journal: Structure / Year: 2002 Title: The Structure of the Rlmb 23S Rrna Methyltransferase Reveals a New Methyltransferase Fold with a Unique Knot Authors: Michel, G. / Sauve, V. / Larocque, R. / Li, Y. / Matte, A. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gz0.cif.gz | 344 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gz0.ent.gz | 288.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gz0 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gz0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27944.881 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MC1061 P3 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DL41(DE3) References: UniProt: P39290, UniProt: P63177*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases #2: Water | ChemComp-HOH / | Compound details | HIS-TAG, SELEMETHIO | |
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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: 2.249 Å3/Da / Density % sol: 43 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: PEG400, TRIS-HCL, pH 7.50 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 17, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47 Å / Num. obs: 286761 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.06 % / Biso Wilson estimate: 43 Å2 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 47 Å / Num. obs: 70653 / Redundancy: 4.06 % / Num. measured all: 286761 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.371 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→46.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1925218.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.7186 Å2 / ksol: 0.334869 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→46.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 47 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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