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Yorodumi- PDB-3va0: Crystal structure of RNase T in complex with a di-nucleotide prod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3va0 | ||||||
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Title | Crystal structure of RNase T in complex with a di-nucleotide product (GG) with one Mg in the active site | ||||||
Components |
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Keywords | HYDROLASE/DNA / DEDD nucleases family / exo-nuclease / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response ...rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response / magnesium ion binding / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å | ||||||
Authors | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes Authors: Hsiao, Y.-Y. / Duh, Y. / Chen, Y.P. / Wang, Y.T. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3va0.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3va0.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 3va0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/3va0 ftp://data.pdbj.org/pub/pdb/validation_reports/va/3va0 | HTTPS FTP |
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-Related structure data
Related structure data | 3v9sC 3v9uC 3v9wC 3v9xC 3v9zC 3va3C 3ngyS 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: 25719.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: DNA chain | Mass: 613.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct #3: Chemical | #4: Chemical | ChemComp-CO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.2M Magnesiumformate dihydrate, 0.1M Sodium acetate trihydrate, 18%(w/v) Polyethylene glycol monomethyl ester 5000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 24276 / Num. obs: 24276 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.074 / Net I/σ(I): 10.04 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.47 / Num. unique all: 2143 / Rsym value: 0.232 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NGY Resolution: 2.201→28.389 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8275 / SU ML: 0.63 / σ(F): 0 / Phase error: 23.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.598 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.06 Å2 / Biso mean: 21.0732 Å2 / Biso min: 9.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.201→28.389 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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