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- PDB-5zog: Crystal Structure of R192F hFen1 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5zog
TitleCrystal Structure of R192F hFen1 in complex with DNA
Components
  • DNA (5'-D(*CP*CP*CP*GP*TP*CP*C)-3')
  • DNA (5'-D(*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*GP*AP*T)-3')
  • DNA (5'-D(P*TP*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')
  • Flap endonuclease 1
KeywordsHYDROLASE/DNA / flap endonuclease: gap endonuclease: methylation: posttranslational modification / DNA BINDING PROTEIN / HYDROLASE-DNA complex
Function / homology
Function and homology information


flap endonuclease activity / telomere maintenance via semi-conservative replication / positive regulation of sister chromatid cohesion / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / UV protection / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand ...flap endonuclease activity / telomere maintenance via semi-conservative replication / positive regulation of sister chromatid cohesion / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / UV protection / 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 / DNA replication / chromosome, telomeric region / 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
DNA / DNA (> 10) / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsHan, W. / Hua, Y. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500656 China
CitationJournal: 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
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flap endonuclease 1
B: DNA (5'-D(*CP*CP*CP*GP*TP*CP*C)-3')
C: DNA (5'-D(P*TP*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')
D: DNA (5'-D(*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*GP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)50,8044
Polymers50,8044
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-27 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.330, 244.800, 70.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

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Components

#1: Protein Flap endonuclease 1 / FEN-1 / DNase IV / Flap structure-specific endonuclease 1 / Maturation factor 1 / hFEN-1


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
#2: DNA chain DNA (5'-D(*CP*CP*CP*GP*TP*CP*C)-3')


Mass: 2034.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')


Mass: 5781.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*GP*AP*T)-3')


Mass: 4080.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: PEG 3350, MgCl2, Tris, KCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.365.0940.7132.5323160.7760.79890.7
2.36-2.425.3910.563.2724530.8580.624100
2.42-2.495.3910.4983.6823890.8830.555100
2.49-2.575.330.4194.4123560.9050.468100
2.57-2.655.3630.3395.3522670.9540.37899.7
2.65-2.755.0330.2597.2821670.9630.29199.2
2.75-2.855.3640.1938.5621280.9810.215100
2.85-2.975.3270.1589.9620510.9840.176100
2.97-3.15.330.11513.0319490.9910.129100
3.1-3.255.2670.08116.8918770.9970.0999.8
3.25-3.435.1620.06520.418010.9970.07399.8
3.43-3.634.8530.05524.8716640.9970.06298.6
3.63-3.884.5840.04928.3415780.9970.05697.9
3.88-4.24.8140.03932.6714950.9980.04498.9
4.2-4.65.0380.03436.113530.9980.03899.7
4.6-5.144.9170.03338.0112650.9990.03799.6
5.14-5.934.830.0336.8511270.9990.03499.7
5.93-7.275.0470.02938.359500.9990.033100
7.27-10.284.8640.02343.447600.9990.02599.7
10.28-29.5594.3410.0244.243840.9990.02384.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q8K

3q8k


Resolution: 2.299→29.559 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.19
RfactorNum. reflection% reflection
Rfree0.2313 1740 5.07 %
Rwork0.2087 --
obs0.2098 34301 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.29 Å2 / Biso mean: 63.2635 Å2 / Biso min: 20.45 Å2
Refinement stepCycle: final / Resolution: 2.299→29.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 791 0 85 3359
Biso mean---43.51 -
Num. residues----355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2988-2.36640.25321500.26842493264392
2.3664-2.44280.2391470.24726832830100
2.4428-2.530.27391450.251927132858100
2.53-2.63130.25851510.242726982849100
2.6313-2.7510.31561440.27972695283999
2.751-2.89590.2521390.240427202859100
2.8959-3.07710.25811320.235427422874100
3.0771-3.31440.22061540.222627042858100
3.3144-3.64740.24281490.22152731288099
3.6474-4.1740.24861470.20212719286698
4.174-5.25390.18491520.165127742926100
5.2539-29.56110.19761300.16852889301998

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