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Yorodumi- PDB-5k97: Flap endonuclease 1 (FEN1) D233N with cleaved product fragment an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k97 | |||||||||
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Title | Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+ | |||||||||
Components |
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Keywords | HYDROLASE/DNA / METALLOPROTEIN / REPLICATION / DNA DAMAGE / DNA REPAIR / BASE EXCISION REPAIR / PROTEIN-DNA / 5' NUCLEASE / FEN / PRODUCT / 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 / molecular replacement / Resolution: 2.102 Å | |||||||||
Authors | Tsutakawa, S.E. / Arvai, A.S. / Tainer, J.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2017 Title: Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Authors: Tsutakawa, S.E. / Thompson, M.J. / Arvai, A.S. / Neil, A.J. / Shaw, S.J. / Algasaier, S.I. / Kim, J.C. / Finger, L.D. / Jardine, E. / Gotham, V.J.B. / Sarker, A.H. / Her, M.Z. / Rashid, F. / ...Authors: Tsutakawa, S.E. / Thompson, M.J. / Arvai, A.S. / Neil, A.J. / Shaw, S.J. / Algasaier, S.I. / Kim, J.C. / Finger, L.D. / Jardine, E. / Gotham, V.J.B. / Sarker, A.H. / Her, M.Z. / Rashid, F. / Hamdan, S.M. / Mirkin, S.M. / Grasby, J.A. / Tainer, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k97.cif.gz | 199.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k97.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 5k97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k97_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 5k97_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 5k97_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 5k97_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/5k97 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/5k97 | HTTPS FTP |
-Related structure data
Related structure data | 5kseC 5um9C 5k96 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38510.203 Da / Num. of mol.: 1 / Mutation: D233N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FEN1, RAD2 / Production host: Escherichia coli (E. coli) References: UniProt: P39748, Hydrolases; Acting on ester bonds |
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-DNA chain , 4 types, 4 molecules DEFG
#2: DNA chain | Mass: 5476.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3438.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2058.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 1479.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide synthesis / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 633 molecules
#6: Chemical | ChemComp-SM / #7: Chemical | ChemComp-K / | #8: Chemical | ChemComp-EDO / | #9: Water | ChemComp-HOH / | |
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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: 3.34 Å3/Da / Density % sol: 63.17 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop Details: 24% MPEG 2K, 20% KCl, 5% ethylene glycol, 100 mM HEPES pH 7.5 PH range: ?76.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 39124 / % possible obs: 99.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 42.47 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.025 / Rrim(I) all: 0.095 / Χ2: 6.084 / Net I/av σ(I): 73.898 / Net I/σ(I): 18.4 / Num. measured all: 539312 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.102→34.849 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.102→34.849 Å
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Refine LS restraints |
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LS refinement shell |
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