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- PDB-5zof: Crystal Structure of D181A/R192F hFen1 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5zof
TitleCrystal Structure of D181A/R192F hFen1 in complex with DNA
Components
  • DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*G)-3')
  • DNA (5'-D(*CP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')
  • DNA (5'-D(*GP*CP*CP*CP*GP*TP*CP*C)-3')
  • Flap endonuclease 1Flap structure-specific endonuclease 1
KeywordsHYDROLASE/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 / 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
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: 2.249 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*G)-3')
C: DNA (5'-D(*GP*CP*CP*CP*GP*TP*CP*C)-3')
D: DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8385
Polymers49,7994
Non-polymers391
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-22 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.670, 92.730, 102.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37613.262 Da / Num. of mol.: 1 / Fragment: nuclease core (1-333) / Mutation: D181A, 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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DNA chain , 3 types, 3 molecules BCD

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


Mass: 5477.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*CP*GP*TP*CP*C)-3')


Mass: 2363.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*G)-3')


Mass: 4344.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 11 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
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: 2.24→27.82 Å / Num. obs: 22092 / % possible obs: 98.8 % / Redundancy: 5.74 % / Biso Wilson estimate: 46.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.101 / Χ2: 0.972 / Net I/σ(I): 11.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.7620.5792.1515350.7380.67393.1
2.31-2.375.3870.4733.215670.8770.52599.6
2.37-2.445.9730.4223.815200.9050.46398.7
2.44-2.526.1520.3214.9314940.9520.35198.8
2.52-2.66.1780.2785.6414250.9620.30499.9
2.6-2.696.1690.2096.9513980.9810.22998.8
2.69-2.796.0910.1798.2213570.9870.19599.9
2.79-2.96.1410.14410.0513050.9870.15799.2
2.9-3.036.0620.12811.6712490.9880.1499.4
3.03-3.185.9710.10713.8112120.990.11899.3
3.18-3.355.9470.09416.2211400.9890.10499.9
3.35-3.565.8630.08717.6910910.990.09599.4
3.56-3.85.7890.08318.6210230.9920.09199.7
3.8-4.115.7180.07919.179570.9920.08799.5
4.11-4.55.7120.07619.928920.9930.08499.9
4.5-5.035.6940.07620.068180.9910.08499.6
5.03-5.815.6060.07319.797330.9930.0899.9
5.81-7.125.4790.07319.496180.9910.08100
7.12-10.065.4770.06820.284950.9910.07699
10.06-27.824.8590.06919.182630.990.07787.4

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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: 2.249→27.82 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1114 5.04 %
Rwork0.2353 20972 -
obs0.237 22086 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.83 Å2 / Biso mean: 56.5319 Å2 / Biso min: 24.57 Å2
Refinement stepCycle: final / Resolution: 2.249→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 806 1 10 3107
Biso mean--133.83 52.82 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2491-2.35150.39521440.35072473261796
2.3515-2.47540.3481360.33282598273499
2.4754-2.63030.36851250.31412594271999
2.6303-2.83320.40361430.29552598274199
2.8332-3.1180.32121390.28426172756100
3.118-3.56840.26791260.24712652277899
3.5684-4.49270.22191590.208126472806100
4.4927-27.82250.2191420.182793293599

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