+Open data
-Basic information
Entry | Database: PDB / ID: 7n94 | ||||||
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Title | LINE-1 endonuclease domain complex with DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / endonuclease / non-LTR retrotransposon / HYDROLASE-DNA complex | ||||||
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 / 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: 2.85 Å | ||||||
Authors | Korolev, S. / Miller, I. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease. Authors: Miller, I. / Totrov, M. / Korotchkina, L. / Kazyulkin, D.N. / Gudkov, A.V. / Korolev, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n94.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n94.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 7n94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n94_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 7n94_full_validation.pdf.gz | 473.2 KB | Display | |
Data in XML | 7n94_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 7n94_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/7n94 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/7n94 | HTTPS FTP |
-Related structure data
Related structure data | 7n8kC 7n8sC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 27073.240 Da / Num. of mol.: 2 / Mutation: D145A, Y226K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: O00370, RNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters #2: DNA chain | Mass: 5497.563 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 5533.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6 / Details: 0.1M MES pH 6.0, 0.2M NaCl, 30% Jeffamine ED-2003 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 17800 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 46.43 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.017 / Χ2: 0.93 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.75 / Num. unique obs: 888 / CC1/2: 0.759 / Rpim(I) all: 0.464 / Χ2: 0.715 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vyb Resolution: 2.85→42.92 Å / SU ML: 0.3927 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0256 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→42.92 Å
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Refine LS restraints |
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LS refinement shell |
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