+Open data
-Basic information
Entry | Database: PDB / ID: 5fv7 | ||||||
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Title | Human Fen1 in complex with an N-hydroxyurea compound | ||||||
Components | FLAP ENDONUCLEASE 1Flap structure-specific endonuclease 1 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate ...positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand / exonuclease activity / Early Phase of HIV Life Cycle / PCNA-Dependent Long Patch Base Excision Repair / POLB-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 / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA replication / damaged DNA binding / chromosome, telomeric region / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Exell, J.C. / Thompson, M.J. / Finger, L.D. / Shaw, S.K. / Abbott, W.M. / McWhirter, C. / Debreczeni, J.E. / Jones, C.D. / Nissink, J.W.M. / Ward, T.A. ...Exell, J.C. / Thompson, M.J. / Finger, L.D. / Shaw, S.K. / Abbott, W.M. / McWhirter, C. / Debreczeni, J.E. / Jones, C.D. / Nissink, J.W.M. / Ward, T.A. / Sioberg, C.W.L. / Molina, D.M. / Durant, S.T. / Grasby, J.A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Cellular Active N-Hydroxyurea Fen1 Inhibitors Block Substrate Entry to the Active Site Authors: Exell, J.C. / Thompson, M.J. / Finger, L.D. / Shaw, S.K. / Abbott, W.M. / Mcwhirter, C. / Debreczeni, J.E. / Jones, C.D. / Nissink, J.W.M. / Ward, T.A. / Sioberg, C.W.L. / Molina, D.M. / ...Authors: Exell, J.C. / Thompson, M.J. / Finger, L.D. / Shaw, S.K. / Abbott, W.M. / Mcwhirter, C. / Debreczeni, J.E. / Jones, C.D. / Nissink, J.W.M. / Ward, T.A. / Sioberg, C.W.L. / Molina, D.M. / Durant, S.T. / Grasby, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fv7.cif.gz | 221.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fv7.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/5fv7 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/5fv7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.5201, -0.1276, -0.8445), Vector: |
-Components
#1: Protein | Mass: 39796.570 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-336 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P39748, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-MG / #3: Chemical | #4: 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 | Description: NONE |
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Crystal grow | pH: 7.5 Details: 25% PEG3350, 0.1M MOPS 7.0, 5% 2-PROPANOL, 2% GLYCEROL, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.886 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→49.07 Å / Num. obs: 12396 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.84→2.94 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.5 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→65.29 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.863 / SU B: 47.68 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.54 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.792 Å2
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Refinement step | Cycle: LAST / Resolution: 2.84→65.29 Å
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