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Yorodumi- PDB-2v0s: crystal structure of a hairpin exchange variant (LR1) of the targ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v0s | ||||||
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Title | crystal structure of a hairpin exchange variant (LR1) of the targeting LINE-1 retrotransposon endonuclease | ||||||
Components | LR1 | ||||||
Keywords | TRANSCRIPTION / APE-1 TYPE / ENDONUCLEASE / RETROTRANSPOSITION / RETROTRANSPOSON / PROTEIN ENGINEERING / HYPOTHETICAL PROTEIN | ||||||
Function / homology | Function and homology information retrotransposition / nucleic acid metabolic process / type II site-specific deoxyribonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / catalytic activity / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / DNA recombination / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Repanas, K. / Zingler, N. / Layer, L.E. / Schumann, G.G. / Perrakis, A. / Weichenrieder, O. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v0s.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v0s.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v0s_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 2v0s_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 2v0s_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2v0s_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/2v0s ftp://data.pdbj.org/pub/pdb/validation_reports/v0/2v0s | HTTPS FTP |
-Related structure data
Related structure data | 2v0rC 1vybS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 26767.752 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-193,202-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8TE30, UniProt: O00370*PLUS | ||||||
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#2: Chemical | ChemComp-MN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 44.86 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→80 Å / Num. obs: 23062 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.8→1.89 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VYB Resolution: 1.8→80 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.607 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / 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: 15.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→80 Å
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Refine LS restraints |
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