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- PDB-3v9x: Crystal structure of RNase T in complex with a preferred ssDNA (A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v9x | ||||||
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Title | Crystal structure of RNase T in complex with a preferred ssDNA (AAA) with two Mg in the active site | ||||||
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![]() | HYDROLASE/DNA / DEDD nucleases family / exo-nuclease / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() rRNA 3'-end processing / tRNA 3'-end processing / regulatory ncRNA 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 / tRNA 3'-end processing / regulatory ncRNA 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192 KB | Display | ![]() |
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PDB format | ![]() | 150 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.9 KB | Display | ![]() |
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Full document | ![]() | 502 KB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 54.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v9sC ![]() 3v9uC ![]() 3v9wC ![]() 3v9zC ![]() 3va0C ![]() 3va3C ![]() 3ngyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25719.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: DNA chain | Mass: 2120.448 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic construct #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.7455 Å3/Da / Density % sol: 29.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20%(v/v) 2-Propanol, 0.1M MES monohydrate, 20%(w/v) Polyethylene glycol monomethyl ester 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2010 |
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: 1.9→30 Å / Num. all: 58869 / Num. obs: 58869 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.06 / Net I/σ(I): 25.29 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.98 / Num. unique all: 5942 / Rsym value: 0.353 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NGY Resolution: 1.9→23.27 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8405 / SU ML: 0.49 / σ(F): 1.97 / Phase error: 23.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.647 Å2 / ksol: 0.39 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.88 Å2 / Biso mean: 27.8563 Å2 / Biso min: 10.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→23.27 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: 30
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