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- PDB-3nh2: Crystal structure of RNase T in complex with a stem DNA with a 3'... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nh2 | ||||||
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Title | Crystal structure of RNase T in complex with a stem DNA with a 3' overhang | ||||||
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![]() | HYDROLASE/DNA / exoribonuclease / RNA processing / RNA maturation / protein-DNA interactions / protein-DNA complex / 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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
![]() | ![]() Title: Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation Authors: Hsiao, Y.-Y. / Yang, C.-C. / Lin, C.L. / Lin, J.L.J. / Duh, Y. / 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 | ![]() | 188.4 KB | Display | ![]() |
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PDB format | ![]() | 146.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.4 KB | Display | ![]() |
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Full document | ![]() | 491.3 KB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ngySC ![]() 3ngzC ![]() 3nh0C ![]() 3nh1C 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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3 | ![]()
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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: 2081.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ssDNA / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1% w/v n-Octyl-beta-D-glucoside, 0.1M Sodium citrate tribasic dihydrate, pH 5.5, 22% PEG 4000, 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: Nov 14, 2009 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 35579 / Num. obs: 35579 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.1 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3544 / Rsym value: 0.41 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NGY Resolution: 2.3→26.761 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.806 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.72 / 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 / Bsol: 40.97 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.83 Å2 / Biso mean: 26.2313 Å2 / Biso min: 8.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→26.761 Å
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Refine LS restraints |
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LS refinement shell |
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