+Open data
-Basic information
Entry | Database: PDB / ID: 3ud4 | ||||||
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Title | The C92U mutant c-di-GMP-I riboswitch bound to GpA | ||||||
Components |
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Keywords | SIGNALING PROTEIN/RNA / riboswitch / SIGNALING PROTEIN-RNA 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Smith, K.D. / Strobel, S.A. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer. Authors: Smith, K.D. / Lipchock, S.V. / Strobel, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ud4.cif.gz | 147.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ud4.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ud4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/3ud4 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/3ud4 | HTTPS FTP |
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-Related structure data
Related structure data | 3ucuC 3uczC 3ud3C 3mxhS 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 | THE PROTEIN IS NOT BIOLOGICALLY RELEVANT AND HAS BEEN USED AS A CRYSTALLIZATION CHAPERONE. |
-Components
#1: Protein | Mass: 11340.315 Da / Num. of mol.: 1 / Fragment: RNA binding domain, UNP residues 1-98 / Mutation: Y31H, Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09012 |
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#2: RNA chain | Mass: 29943.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcribed RNA transcript |
#3: RNA chain | Mass: 629.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GpA |
#4: Chemical | ChemComp-MG / |
#5: 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: 2.02 Å3/Da / Density % sol: 39.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 24% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 9403 / Num. obs: 9365 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3MXH Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.798 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.697→2.767 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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