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- PDB-2v0r: crystal structure of a hairpin exchange variant (LTx) of the targ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v0r | ||||||
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Title | crystal structure of a hairpin exchange variant (LTx) of the targeting LINE-1 retrotransposon endonuclease | ||||||
![]() | LTX | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Repanas, K. / Zingler, N. / Layer, L.E. / Schumann, G.G. / Perrakis, A. / Weichenrieder, O. | ||||||
![]() | ![]() Title: Determinants for DNA Target Structure Selectivity of the Human Line-1 Retrotransposon Endonuclease Authors: Repanas, K. / Zingler, N. / Layer, L.E. / Schumann, G.G. / Perrakis, A. / Weichenrieder, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.7 KB | Display | ![]() |
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PDB format | ![]() | 84.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2v0sC ![]() 1vybS 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: 27361.500 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-192,202-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Water | ChemComp-HOH / | ![]() Sequence details | THIS STRUCTURE IS A VARIANT OF THE PDB ENTRY 1VYB: L1 ENDONUCLEASE DOMAIN. THE LOOP REGION 193-201 ...THIS STRUCTURE IS A VARIANT OF THE PDB ENTRY 1VYB: L1 ENDONUCLEA | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.06 % / Description: NONE |
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Crystal grow![]() | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→20 Å / Num. obs: 22873 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1VYB Resolution: 2.3→19.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.859 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.273 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.53 Å
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Refine LS restraints |
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