+Open data
-Basic information
Entry | Database: PDB / ID: 5twk | ||||||||||||
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Title | Crystal Structure of RlmH in Complex with Sinefungin | ||||||||||||
Components | Ribosomal RNA large subunit methyltransferase H | ||||||||||||
Keywords | TRANSFERASE/ANTIBIOTIC / Sinefungin / RNA methyltransferase / SPOUT / pseudouridine / helix 69 / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex | ||||||||||||
Function / homology | Function and homology information 23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / rRNA base methylation / rRNA methylation / ribosome binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Koh, C.S. / Madireddy, R. / Beane, T.J. / Zamore, P.D. / Korostelev, A.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Rep / Year: 2017 Title: Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine. Authors: Koh, C.S. / Madireddy, R. / Beane, T.J. / Zamore, P.D. / Korostelev, A.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5twk.cif.gz | 268.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5twk.ent.gz | 217.2 KB | Display | PDB format |
PDBx/mmJSON format | 5twk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5twk_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5twk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5twk_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 5twk_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/5twk ftp://data.pdbj.org/pub/pdb/validation_reports/tw/5twk | HTTPS FTP |
-Related structure data
Related structure data | 5twjC 1ns5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18293.111 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rlmH / Production host: Escherichia coli (E. coli) References: UniProt: B7MFQ9, UniProt: P0A8I8*PLUS, 23S rRNA (pseudouridine1915-N3)-methyltransferase #2: Chemical | ChemComp-SFG / #3: 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: 2.02 Å3/Da / Density % sol: 39.05 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-bicine buffer (pH 8.5), 0.09 M NaF, 0.09 M NaBr, 0.09 M NaI, 20% v/v PEG 550 MME, 10% w/v PEG 20,000 in the presence of 2 mM Sinefungin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.1 Å / Num. obs: 34496 / % possible obs: 99.24 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06791 / Net I/σ(I): 17.66 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 3405 / % possible all: 93.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NS5 Resolution: 2.1→39.084 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 25.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.084 Å
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Refine LS restraints |
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LS refinement shell |
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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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