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Yorodumi- PDB-3t3n: Molecular basis for the recognition and cleavage of RNA (UUCCGU) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t3n | ||||||
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Title | Molecular basis for the recognition and cleavage of RNA (UUCCGU) by the bifunctional 5'-3' exo/endoribonuclease RNase J | ||||||
Components |
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Keywords | HYDROLASE/RNA / PROTEIN-RNA COMPLEX / Metallo-beta-lactamase / RNase J / Endoribonuclease / 5'-3' Exoribonuclease / Metal dependent hydrolase / RNA / hydrolase / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å | ||||||
Authors | Dorleans, A. / Li de la Sierra-Gallay, I. / Piton, J. / Zig, L. / Gilet, L. / Putzer, H. / Condon, C. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J. Authors: Dorleans, A. / Li de la Sierra-Gallay, I. / Piton, J. / Zig, L. / Gilet, L. / Putzer, H. / Condon, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t3n.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t3n.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 3t3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t3n_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
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Full document | 3t3n_full_validation.pdf.gz | 471.6 KB | Display | |
Data in XML | 3t3n_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 3t3n_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/3t3n ftp://data.pdbj.org/pub/pdb/validation_reports/t3/3t3n | HTTPS FTP |
-Related structure data
Related structure data | 3t3oC 3bk1S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 62612.379 Da / Num. of mol.: 1 / Mutation: H77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Gene: ttc0775, TT_C0775 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q72JJ7, Hydrolases |
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#2: RNA chain | Mass: 1913.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 16-nt 2'-O-methylated RNA |
#3: Chemical | ChemComp-ZN / |
#4: 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: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2-4% PEG 4K, 0.02M ammonium sulfate, 0.1M Na-MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2010 Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal |
Radiation | Monochromator: cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→55 Å / Num. all: 12981 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 72.03 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.67 |
Reflection shell | Resolution: 3.1→3.25 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.93 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BK1 Resolution: 3.09→54.41 Å / Cor.coef. Fo:Fc: 0.9262 / Cor.coef. Fo:Fc free: 0.8728 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 77.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.585 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→54.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.09→3.38 Å / Total num. of bins used: 6
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