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- PDB-4rea: A Nuclease DNA complex -

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Basic information

Entry
Database: PDB / ID: 4rea
TitleA Nuclease DNA complex
Components
  • DNA (5'-D(*TP*GP*CP*TP*CP*GP*CP*CP*AP*C)-3')
  • DNA (5'-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')
  • Fanconi-associated nuclease 1
KeywordsHydrolase/DNA / HJC / TPR / SAP / structural specific nuclease / FANCD2 / 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
DNA / DNA (> 10) / Fanconi-associated nuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fanconi-associated nuclease 1
A: Fanconi-associated nuclease 1
C: DNA (5'-D(*TP*GP*CP*TP*CP*GP*CP*CP*AP*C)-3')
D: DNA (5'-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*C)-3')
E: DNA (5'-D(P*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)158,5895
Polymers158,5895
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.960, 100.960, 115.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 371 - 1009 / Label seq-ID: 1 - 639

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

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


Mass: 2980.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*C)-3')


Mass: 3086.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3')


Mass: 5214.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 300 K / Method: micro-batch under oil
Details: 0.1-0.2M KSCN, 18-22% PEG 3350, 0.1M BisTris-propane, micro-batch under oil, temperature 300K
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 28, 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, L10.49
11K, H, -L20.51
ReflectionResolution: 3.8→50.5 Å / Num. all: 12265 / Num. obs: 11982 / % possible obs: 97.69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Rmerge(I) obs: 0.207 / Net I/σ(I): 2.6
Reflection shellResolution: 3.8→3.95 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 0.1 / % possible all: 85.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.81→50.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 34.485 / SU ML: 0.487 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 635 5 %RANDOM
Rwork0.2427 ---
obs0.2443 11982 97.69 %-
all-12265 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 459.92 Å2 / Biso mean: 221.265 Å2 / Biso min: 125.14 Å2
Baniso -1Baniso -2Baniso -3
1--25.19 Å20 Å20 Å2
2---25.19 Å20 Å2
3---50.38 Å2
Refinement stepCycle: LAST / Resolution: 3.81→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9500 754 0 0 10254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910565
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.88814439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88551174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06323.218463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.563151749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.661585
X-RAY DIFFRACTIONr_chiral_restr0.1150.21581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217670
Refine LS restraints NCS

Ens-ID: 1 / Number: 92 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.32 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 3.81→3.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.533 26 -
Rwork0.477 752 -
all-778 -
obs--82.24 %

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