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Open data
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Basic information
Entry | Database: PDB / ID: 1vyb | ||||||
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Title | Endonuclease domain of human LINE1 ORF2p | ||||||
![]() | ORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN | ||||||
![]() | TRANSFERASE / ENDONUCLEASE / APE-1 TYPE / RETROTRANSPOSITION / RETROTRANSPOSON / RNA-DIRECTED DNA POLYMERASE | ||||||
Function / homology | ![]() retrotransposition / nucleic acid metabolic process / type II site-specific deoxyribonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / DNA recombination / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weichenrieder, O. / Repanas, K. / Perrakis, A. | ||||||
![]() | ![]() Title: Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon. Authors: Weichenrieder, O. / Repanas, K. / Perrakis, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116 KB | Display | ![]() |
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PDB format | ![]() | 89.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.9 KB | Display | ![]() |
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Full document | ![]() | 478.9 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dewS S: Starting model for refinement |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.39, 0.028, -0.92), Vector: |
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Components
#1: Protein | Mass: 27151.244 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE DOMAIN, RESIDUES 1-238 Source method: isolated from a genetically manipulated source Details: NOT OFFICIALLY ASSIGNED TO EC 4.2.99.18, BUT THAT IS THE CLOSEST GROUP Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45 % |
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Crystal grow | pH: 7 / Details: pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 685558 / % possible obs: 97.5 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.4 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DEW Resolution: 1.8→20.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.047 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20.1 Å
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Refine LS restraints |
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