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Yorodumi- PDB-4blw: Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4blw | ||||||
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Title | Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in complex with S-adenosylhomocysteine (AdoHcy) and Adenosine monophosphate (AMP) | ||||||
Components | RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J | ||||||
Keywords | TRANSFERASE / N6-METHYLADENINE / ROSSMANN-LIKE FOLD / SUBDOMAIN INSERTION | ||||||
Function / homology | Function and homology information 23S rRNA (adenine2030-N6)-methyltransferase / 23S rRNA (adenine(2030)-N(6))-methyltransferase activity / rRNA (adenine-N6-)-methyltransferase activity / carbon utilization / rRNA base methylation / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Punekar, A.S. / Liljeruhm, J. / Shepherd, T.R. / Forster, A.C. / Selmer, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Structural and Functional Insights Into the Molecular Mechanism of Rrna M6A Methyltransferase Rlmj. Authors: Punekar, A.S. / Liljeruhm, J. / Shepherd, T.R. / Forster, A.C. / Selmer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4blw.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4blw.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 4blw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4blw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4blw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4blw_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 4blw_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/4blw ftp://data.pdbj.org/pub/pdb/validation_reports/bl/4blw | HTTPS FTP |
-Related structure data
Related structure data | 4bluSC 4blvC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-1, -0.0035, 0.0062), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33088.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SPECIFICALLY MONOMETHYLATES THE ADENINE IN POSITION 2030 OF 23S RRNA Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PEXP5-CT/TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P37634, 23S rRNA (adenine2030-N6)-methyltransferase |
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-Non-polymers , 7 types, 359 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2 M SODIUM SULFATE DECAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.3776 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3776 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46 Å / Num. obs: 41777 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 23.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BLU Resolution: 1.95→45.951 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 20.85 / Stereochemistry target values: ML Details: RESIDUE 280 IN CHAIN B IS DISORDERED AND WAS NOT MODELED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.951 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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