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- PDB-5fv7: Human Fen1 in complex with an N-hydroxyurea compound -

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Basic information

Entry
Database: PDB / ID: 5fv7
TitleHuman Fen1 in complex with an N-hydroxyurea compound
ComponentsFLAP ENDONUCLEASE 1
KeywordsHYDROLASE
Function / homology
Function and homology information


flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / UV protection / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand ...flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / UV protection / DNA replication, removal of RNA primer / 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 / RNA-DNA hybrid ribonuclease activity / double-strand break repair / manganese ion binding / double-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / DNA repair / nucleolus / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
Chem-R3Z / Flap endonuclease 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsExell, 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.
CitationJournal: 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
DepositionFeb 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAP ENDONUCLEASE 1
B: FLAP ENDONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3558
Polymers79,5932
Non-polymers7626
Water181
1
A: FLAP ENDONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1784
Polymers39,7971
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FLAP ENDONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1784
Polymers39,7971
Non-polymers3813
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.339, 50.193, 66.945
Angle α, β, γ (deg.)102.06, 94.01, 90.74
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.5201, -0.1276, -0.8445), (-0.1126, -0.9904, 0.08026), (-0.8466, 0.05332, -0.5295)
Vector: 19, 2.756, 25.39)

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Components

#1: Protein FLAP ENDONUCLEASE 1 / FEN-1 / DNASE IV / FLAP STRUCTURE-SPECIFIC ENDONUCLEASE 1 / MATURATION FACTOR 1 / MF1 / HFEN-1


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 / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-R3Z / 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione


Mass: 332.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12N2O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDescription: NONE
Crystal growpH: 7.5
Details: 25% PEG3350, 0.1M MOPS 7.0, 5% 2-PROPANOL, 2% GLYCEROL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.886
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.84→2.94 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.5 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.30021 576 4.8 %RANDOM
Rwork0.23387 ---
obs0.23712 11422 92.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.792 Å2
Baniso -1Baniso -2Baniso -3
1--4.3 Å2-0.46 Å2-1.13 Å2
2---2.75 Å20.68 Å2
3---7.17 Å2
Refinement stepCycle: LAST / Resolution: 2.84→65.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 50 1 4260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.014352
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.985907
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0385551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96824.65176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33315709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0351519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023301
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 27 -
Rwork0.309 820 -
obs--87.5 %

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