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- PDB-4rec: A nuclease-DNA complex form 3 -

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Basic information

Entry
Database: PDB / ID: 4rec
TitleA nuclease-DNA complex form 3
Components
  • DNA (40-MER)
  • 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
IODIDE 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: 2.2 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fanconi-associated nuclease 1
B: DNA (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3515
Polymers85,9712
Non-polymers3813
Water4,414245
1
A: Fanconi-associated nuclease 1
hetero molecules

A: Fanconi-associated nuclease 1
B: DNA (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,3869
Polymers159,6253
Non-polymers7616
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation3_744-x+2,y-1/2,-z-1/21
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.910, 109.600, 115.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 1 / 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 (40-MER)


Mass: 12316.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 300 K / Method: micro-batch under oil
Details: 0.1M potassium iodide, 0.1mM spermidine, 18% PEG3350, 0.1M BisTris propane, micro-batch under oil, temperature 300K
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→79.6 Å / Num. all: 89742 / Num. obs: 89740 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 55.68 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.3 Å / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: an initial model phased by a low-resolution iodine-anomalous dataset

Resolution: 2.2→79.6 Å / SU ML: 0.46 / σ(F): 1.04 / Phase error: 34.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 2983 3.32 %
Rwork0.2154 --
obs0.2167 89740 99.91 %
all-89742 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.44 Å2 / Biso mean: 68.7619 Å2 / Biso min: 28.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→79.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 814 3 245 5840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095801
X-RAY DIFFRACTIONf_angle_d1.1528009
X-RAY DIFFRACTIONf_chiral_restr0.048895
X-RAY DIFFRACTIONf_plane_restr0.006884
X-RAY DIFFRACTIONf_dihedral_angle_d21.5522211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.23610.44451410.447541584299
2.2361-2.27460.43351430.424541134256
2.2746-2.3160.44381410.392341394280
2.316-2.36050.39851580.375440684226
2.3605-2.40870.4121440.362841404284
2.4087-2.46110.36471480.332541224270
2.4611-2.51840.35471310.316141374268
2.5184-2.58130.34511440.304741554299
2.5813-2.65110.37271470.294641124259
2.6511-2.72920.35671300.288641404270
2.7292-2.81730.3241540.269141254279
2.8173-2.91790.28951240.238141624286
2.9179-3.03480.27051470.229541024249
3.0348-3.17290.25851470.2341294276
3.1729-3.34020.3431310.22541394270
3.3402-3.54950.28791470.208741524299
3.5495-3.82350.2521450.183741154260
3.8235-4.20830.19581420.178941494291
4.2083-4.81720.19431370.160641304267
4.8172-6.06880.21061400.1941354275
6.0688-79.67220.18981420.177441354277

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