+Open data
-Basic information
Entry | Database: PDB / ID: 5zog | ||||||
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Title | Crystal Structure of R192F hFen1 in complex with DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / flap endonuclease: gap endonuclease: methylation: posttranslational modification / DNA BINDING PROTEIN / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / nucleic acid metabolic process / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / UV protection / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) ...positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / nucleic acid metabolic process / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / UV protection / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand / 5'-3' exonuclease activity / exonuclease activity / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / double-strand break repair via homologous recombination / memory / double-strand break repair / RNA-DNA hybrid ribonuclease activity / double-stranded DNA binding / manganese ion binding / chromosome, telomeric region / DNA replication / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / nucleolus / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å | ||||||
Authors | Han, W. / Hua, Y. / Zhao, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural basis of 5' flap recognition and protein-protein interactions of human flap endonuclease 1. Authors: Xu, H. / Shi, R. / Han, W. / Cheng, J. / Xu, X. / Cheng, K. / Wang, L. / Tian, B. / Zheng, L. / Shen, B. / Hua, Y. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zog.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zog.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zog_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 5zog_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 5zog_validation.xml.gz | 15 KB | Display | |
Data in CIF | 5zog_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zog ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zog | HTTPS FTP |
-Related structure data
Related structure data | 5zodC 5zoeC 5zofC 3q8kS 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: 38907.695 Da / Num. of mol.: 1 / Fragment: nuclease core (1-333) / Mutation: R192F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FEN1, RAD2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS References: UniProt: P39748, Hydrolases; Acting on ester bonds |
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#2: DNA chain | Mass: 2034.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 5781.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 4080.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: PEG 3350, MgCl2, Tris, KCl |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.299→29.559 Å / Num. obs: 34330 / % possible obs: 98.8 % / Redundancy: 5.143 % / Biso Wilson estimate: 39.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.079 / Χ2: 1.02 / Net I/σ(I): 16.12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q8K Resolution: 2.299→29.559 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.29 Å2 / Biso mean: 63.2635 Å2 / Biso min: 20.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.299→29.559 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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