+Open data
-Basic information
Entry | Database: PDB / ID: 6fz0 | ||||||
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Title | Crystal structure of the metY SAM V riboswitch | ||||||
Components | metY SAM V (53-MER) | ||||||
Keywords | RNA / SAM V riboswitch / pseudoknot / gene regulation | ||||||
Function / homology | S-ADENOSYLMETHIONINE / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Candidatus Pelagibacter ubique HTCC1062 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.499 Å | ||||||
Authors | Huang, L. / Lilley, D.M.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structure and ligand binding of the SAM-V riboswitch. Authors: Huang, L. / Lilley, D.M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fz0.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fz0.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fz0_validation.pdf.gz | 753 KB | Display | wwPDB validaton report |
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Full document | 6fz0_full_validation.pdf.gz | 754.9 KB | Display | |
Data in XML | 6fz0_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 6fz0_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/6fz0 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/6fz0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 17126.105 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Candidatus Pelagibacter ubique HTCC1062 (bacteria) References: GenBank: 71061822 |
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-Non-polymers , 5 types, 18 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-SAM / | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2MPotassium chloride 0.01MCalcium chloride dihydrate 0.05MBis-Tris7.0 40% v/vPEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9196 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 2.499→44.113 Å / Num. obs: 15977 / % possible obs: 100 % / Observed criterion σ(I): 2.1 / Redundancy: 13.8 % / Biso Wilson estimate: 74.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.023 / Rrim(I) all: 0.086 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 428 / CC1/2: 0.4 / Rpim(I) all: 0.276 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.499→44.113 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.15 / 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: 2.499→44.113 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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