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- PDB-4blu: Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4blu | ||||||
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Title | Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ | ||||||
![]() | RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J | ||||||
![]() | TRANSFERASE / N6-METHYLADENINE / ROSSMANN-LIKE FOLD / SUBDOMAIN INSERTION | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Punekar, A.S. / Liljeruhm, J. / Shepherd, T.R. / Forster, A.C. / Selmer, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 111 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494.6 KB | Display | ![]() |
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Full document | ![]() | 502.7 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 44 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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:
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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.) ![]() ![]() ![]() ![]() References: UniProt: P37634, 23S rRNA (adenine2030-N6)-methyltransferase |
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-Non-polymers , 6 types, 580 molecules ![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 6, 2012 / Details: PT COATED MIRRORS |
Radiation | Monochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 48904 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.4 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: RESIDUES 53-55 IN CHAIN B ARE DISORDERED AND WERE 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: 14.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→40.025 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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