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Yorodumi- PDB-3diq: Crystallization of the Thermotoga maritima lysine riboswitch boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3diq | ||||||
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Title | Crystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine | ||||||
Components | RNA (174-MER) | ||||||
Keywords | RNA / riboswitch / Lysine | ||||||
Function / homology | L-HOMOARGININE / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / REFMAC / Resolution: 2.7 Å | ||||||
Authors | serganov, A.A. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structural insights into amino acid binding and gene control by a lysine riboswitch. Authors: Serganov, A. / Huang, L. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3diq.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3diq.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 3diq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3diq_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
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Full document | 3diq_full_validation.pdf.gz | 427.8 KB | Display | |
Data in XML | 3diq_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3diq_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/3diq ftp://data.pdbj.org/pub/pdb/validation_reports/di/3diq | HTTPS FTP |
-Related structure data
Related structure data | 3digC 3dilSC 3dimC 3dioC 3dirC 3disC 3dixC 3diyC 3dizC 3dj0C 3dj2C 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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1 |
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Unit cell |
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-Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 56635.598 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: In vitro transcribed RNA from the Thermotoga maritima MSB8 asd gene |
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-Non-polymers , 5 types, 55 molecules
#2: Chemical | ChemComp-K / | ||||||
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#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-HRG / | #5: Chemical | ChemComp-1PE / | #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: 2.62 Å3/Da / Density % sol: 53.02 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 18% PEG 4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 17041 / Num. obs: 16172 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1662 / Num. unique obs: 1479 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: REFMAC Starting model: pdb entry 3DIL Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 11.885 / SU ML: 0.247 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.338 / 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 mean: 24.898 Å2
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Refine analyze | Luzzati coordinate error obs: 0.247 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Rfactor Rfree error: 0.338 / Total num. of bins used: 20
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