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- PDB-4reb: Structural Insights into 5' Flap DNA Unwinding and Incision by th... -

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Basic information

Entry
Database: PDB / ID: 4reb
TitleStructural Insights into 5' Flap DNA Unwinding and Incision by the Human FAN1 Dimer
Components
  • DNA (5'-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')
  • DNA (5'-D(P*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')
  • DNA (5'-D(P*GP*TP*GP*GP*CP*GP*AP*GP*C)-3')
  • Fanconi-associated nuclease 1
KeywordsHydrolase/DNA / HJC / TPR / SAP / structure specific nuclease / FANCID2 / nucleus / Hydrolase-DNA complex
Function / homology
Function and homology information


flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / intercellular bridge / interstrand cross-link repair / nucleotide-excision repair ...flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / intercellular bridge / interstrand cross-link repair / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / DNA repair / magnesium ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain ...: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain / VRR_NUC / Rad18-like CCHC zinc finger / tRNA endonuclease-like domain superfamily / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile.
Similarity search - Domain/homology
SAMARIUM (III) ION / DNA / DNA (> 10) / Fanconi-associated nuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsZhao, Q. / Xue, X. / Longerich, S. / Sung, P. / Xiong, Y.
CitationJournal: Nat Commun / Year: 2014
Title: Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer.
Authors: Zhao, Q. / Xue, X. / Longerich, S. / Sung, P. / Xiong, Y.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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
D: DNA (5'-D(P*GP*TP*GP*GP*CP*GP*AP*GP*C)-3')
E: DNA (5'-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')
F: DNA (5'-D(P*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')
A: Fanconi-associated nuclease 1
H: Fanconi-associated nuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,5487
Polymers159,2475
Non-polymers3012
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.770, 104.770, 127.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 371 - 1008 / Label seq-ID: 1 - 638

Dom-IDAuth asym-IDLabel asym-ID
1AD
2HE

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Components

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


Mass: 2796.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')


Mass: 6136.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')


Mass: 3005.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein Fanconi-associated nuclease 1 / FANCD2/FANCI-associated nuclease 1 / Myotubularin-related protein 15


Mass: 73653.875 Da / Num. of mol.: 2 / Fragment: UNP residues 373-1017 / Mutation: D960A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAN1, KIAA1018, MTMR15 / Plasmid: pMAT9s / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y2M0, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, phosphodiesterase I
#5: Chemical ChemComp-SM / SAMARIUM (III) ION / Samarium


Mass: 150.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sm

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 300 K / Method: micro-batch under oil
Details: 0.1mM spermidine, 1% 1,6-Hexanediol, 22-24% PEG 3350, 0.1M BisTris Propane, micro-batch under oil, temperature 300K
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.495
11K, H, -L20.505
ReflectionResolution: 4.2→90.7 Å / Num. all: 10865 / Num. obs: 10793 / % possible obs: 99.345 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.8
Reflection shellResolution: 4.2→4.31 Å / % possible all: 99.88

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→90.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.905 / SU B: 40.899 / SU ML: 0.578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 566 5 %RANDOM
Rwork0.2304 ---
obs0.2321 10793 99.34 %-
all-10865 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 460.28 Å2 / Biso mean: 297.363 Å2 / Biso min: 211.23 Å2
Baniso -1Baniso -2Baniso -3
1--33.93 Å20 Å20 Å2
2---33.93 Å20 Å2
3---67.85 Å2
Refinement stepCycle: LAST / Resolution: 4.2→90.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9295 801 2 0 10098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910413
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.88114245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91351145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0523.084454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.912151706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1291585
X-RAY DIFFRACTIONr_chiral_restr0.1070.21553
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217546
Refine LS restraints NCS

Ens-ID: 1 / Number: 5563 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.22 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2H
LS refinement shellResolution: 4.2→4.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 44 -
Rwork0.469 802 -
all-846 -
obs--99.88 %

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