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Yorodumi- PDB-5hw4: Crystal structure of Escherichia coli 16S rRNA methyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hw4 | ||||||
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Title | Crystal structure of Escherichia coli 16S rRNA methyltransferase RsmI in complex with AdoMet | ||||||
Components | Ribosomal RNA small subunit methyltransferase I | ||||||
Keywords | TRANSFERASE / RNA methylation / AdoMet-dependent methyltransferase / ribosome P-site | ||||||
Function / homology | Function and homology information 16S rRNA (cytidine1402-2'-O)-methyltransferase / : / rRNA (cytosine-2'-O-)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.211 Å | ||||||
Authors | Zhao, M. / Zhang, H. / Dong, Y. / Gong, Y. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI Authors: Zhao, M. / Zhang, H. / Liu, G. / Wang, L. / Wang, J. / Gao, Z. / Dong, Y. / Zhang, L. / Gong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hw4.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hw4.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hw4_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5hw4_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5hw4_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 5hw4_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/5hw4 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hw4 | HTTPS FTP |
-Related structure data
Related structure data | 3kwpS 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: 27247.191 Da / Num. of mol.: 3 / Fragment: UNP residues 12-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rsmI, yraL, b3146, JW3115 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P67087, 16S rRNA (cytidine1402-2'-O)-methyltransferase #2: Chemical | #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: 3.33 Å3/Da / Density % sol: 63.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M DL-Malic acid, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 46162 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.535 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KWP Resolution: 2.211→34.943 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.211→34.943 Å
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Refine LS restraints |
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LS refinement shell |
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