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Open data
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Basic information
Entry | Database: PDB / ID: 4kaz | ||||||
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Title | Crystal structure of RNase T in complex with a Y structured DNA | ||||||
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![]() | Hydrolase/dna / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() tRNA 3'-end processing / RNA exonuclease activity, producing 5'-phosphomonoesters / DNA replication proofreading / 3'-5' exonuclease activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
![]() | ![]() Title: Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways. Authors: Hsiao, Y.Y. / Fang, W.H. / Lee, C.C. / Chen, Y.P. / Yuan, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.9 KB | Display | ![]() |
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PDB format | ![]() | 47.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 295.4 KB | Display | ![]() |
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Full document | ![]() | 297 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kb0C ![]() 4kb1C ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 25719.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P30014, ![]() | ||
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#2: DNA chain | Mass: 6052.890 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.99 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% v/v 2-Propanol, 0.1 M MES monohydrate, 20% w/v Polyethylene glycol monomethyl ester 2000 , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 3, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→30 Å / Num. all: 20966 / Num. obs: 20966 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rsym value: 0.091 / Net I/σ(I): 32.23 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.92 / Num. unique all: 2070 / Rsym value: 0.457 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3NGY Resolution: 1.9→28.767 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 19.69 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.767 Å
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Refine LS restraints |
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LS refinement shell |
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