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Yorodumi- PDB-3l8u: Crystal structure of SMU.1707c, a putative rRNA methyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l8u | ||||||
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Title | Crystal structure of SMU.1707c, a putative rRNA methyltransferase from streptococcus mutans UA159 | ||||||
Components | Putative rRNA methylase | ||||||
Keywords | TRANSFERASE / streptococcus mutans / methyltransferase / knotted protein | ||||||
Function / homology | Function and homology information tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gao, X.-Z. / Wang, K.-T. / Su, X.-D. | ||||||
Citation | Journal: To be published Title: Crystal structure of SMU.1707c, a putative rRNA methyltransferase from streptococcus mutans UA159 Authors: Gao, X.-Z. / Wang, K.-T. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l8u.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l8u.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 3l8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l8u_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 3l8u_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 3l8u_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3l8u_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/3l8u ftp://data.pdbj.org/pub/pdb/validation_reports/l8/3l8u | HTTPS FTP |
-Related structure data
Related structure data | 3e5yS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21190.129 Da / Num. of mol.: 2 / Mutation: M140V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_1707c / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DSR4 #2: 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: 2.83 Å3/Da / Density % sol: 56.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.5M (NH4)2SO4, 0.1M Bis-tris pH7.0, 0.7% beta-OG , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 31965 / Num. obs: 31772 / % possible obs: 99.3 % / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E5Y Resolution: 2→35.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.696 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.55 Å2 / Biso mean: 41.124 Å2 / Biso min: 22.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Total num. of bins used: 20
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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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