+Open data
-Basic information
Entry | Database: PDB / ID: 4yb1 | ||||||
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Title | 20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP | ||||||
Components |
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Keywords | RNA/RNA BINDING PROTEIN / riboswitch / 3' / 3'-cGAMP / spinach / RNA structure / c-di-GMP / RNA-RNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.081 Å | ||||||
Authors | Ren, A.M. / Patel, D.J. / Rajashankar, R.K. | ||||||
Citation | Journal: Cell Rep / Year: 2015 Title: Structural Basis for Molecular Discrimination by a 3',3'-cGAMP Sensing Riboswitch. Authors: Ren, A. / Wang, X.C. / Kellenberger, C.A. / Rajashankar, K.R. / Jones, R.A. / Hammond, M.C. / 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 | 4yb1.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yb1.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 4yb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4yb1 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4yb1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 29460.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Production host: in vitro transcription vector pT7-Fluc(deltai) (others) |
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#2: Protein | Mass: 10695.579 Da / Num. of mol.: 1 / Fragment: UNP residues 7-97 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09012 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-4BW / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Na-citrate pH 5.5, 5% PEG1000, 35% iso-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→46.8 Å / Num. obs: 17467 / % possible obs: 75.2 % / Observed criterion σ(I): 0.6 / Redundancy: 2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.08→2.14 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 0.6 / % possible all: 42.2 |
-Processing
Software |
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Refinement | Resolution: 2.081→43.722 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.19 / 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: 2.081→43.722 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 9.7237 Å / Origin y: -2.7309 Å / Origin z: 48.4783 Å
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Refinement TLS group | Selection details: all |