+Open data
-Basic information
Entry | Database: PDB / ID: 3ger | ||||||
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Title | Guanine riboswitch bound to 6-chloroguanine | ||||||
Components | Guanine riboswitch | ||||||
Keywords | RNA / riboswitch / mRNA / guanine / RNA-ligand complex / double helix / three-way junction / base triple | ||||||
Function / homology | 6-chloroguanine / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Gilbert, S.D. / Batey, R.T. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Adaptive ligand binding by the purine riboswitch in the recognition of Guanine and adenine analogs Authors: Gilbert, S.D. / Reyes, F.E. / Edwards, A.L. / Batey, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ger.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ger.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ger.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ger_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
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Full document | 3ger_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 3ger_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3ger_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/3ger ftp://data.pdbj.org/pub/pdb/validation_reports/ge/3ger | HTTPS FTP |
-Related structure data
Related structure data | 3fo4C 3fo6C 3g4mC 3gaoC 3gesC 3gogC 3gotC 1u8d 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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Details | Coordinates for a complete multimer representing the known biologically significant monomeric state of the molecule are given. |
-Components
#1: RNA chain | Mass: 21506.783 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence was engineered based on the guanine riboswitch in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis. | ||
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#2: Chemical | ChemComp-6GU / | ||
#3: Chemical | ChemComp-ACT / | ||
#4: Chemical | ChemComp-NCO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22.5 % PEG 3K, 560 mM ammonium acetate, 12 mM cobalt hexammine, 10 mM K+ HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.916 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2005 |
Radiation | Monochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→20 Å / Num. obs: 27356 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 6.73 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.08 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 5.49 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2589 / Rsym value: 0.377 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1U8D 1u8d Resolution: 1.7→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1593677.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.6426 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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