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- PDB-2aq0: Solution structure of the human homodimeric dna repair protein XPF -

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Basic information

Entry
Database: PDB / ID: 2aq0
TitleSolution structure of the human homodimeric dna repair protein XPF
ComponentsDNA repair endonuclease XPF
KeywordsDNA REPAIR / HYDROLASE / nmr spectroscopy
Function / homology
Function and homology information


negative regulation of double-stranded telomeric DNA binding / negative regulation of telomere maintenance / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair complex / resolution of meiotic recombination intermediates / single-stranded DNA endodeoxyribonuclease activity ...negative regulation of double-stranded telomeric DNA binding / negative regulation of telomere maintenance / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair complex / resolution of meiotic recombination intermediates / single-stranded DNA endodeoxyribonuclease activity / UV protection / negative regulation of telomere maintenance via telomere lengthening / HDR through Single Strand Annealing (SSA) / TFIID-class transcription factor complex binding / response to UV / telomere maintenance / DNA endonuclease activity / regulation of autophagy / promoter-specific chromatin binding / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair via nonhomologous end joining / Dual incision in TC-NER / cellular response to UV / single-stranded DNA binding / damaged DNA binding / chromosome, telomeric region / Hydrolases; Acting on ester bonds / DNA repair / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
DNA repair protein XPF / : / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA repair endonuclease XPF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics; simulated annealing
AuthorsDas, D. / Tripsianes, K. / Folkers, G. / Jaspers, N.G. / Hoeijmakers, J.H. / Kaptein, R. / Boelens, R.
CitationJournal: Proteins / Year: 2008
Title: The HhH domain of the human DNA repair protein XPF forms stable homodimers
Authors: Das, D. / Tripsianes, K. / Jaspers, N.G. / Hoeijmakers, J.H. / Kaptein, R. / Boelens, R. / Folkers, G.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair endonuclease XPF
B: DNA repair endonuclease XPF


Theoretical massNumber of molelcules
Total (without water)18,4612
Polymers18,4612
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein DNA repair endonuclease XPF / E.C.3.1.-.- / DNA excision repair protein ERCC-4 / DNA-repair protein complementing XP-F cell / Xeroderma ...DNA excision repair protein ERCC-4 / DNA-repair protein complementing XP-F cell / Xeroderma pigmentosum group F complementing protein


Mass: 9230.518 Da / Num. of mol.: 2 / Fragment: residues 823-905
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC4, ERCC11, XPF / Production host: Escherichia coli (E. coli)
References: UniProt: Q92889, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D-(H)NCH NOESY HSQC
1412D-15N-separated-(13c)aromatic (1H-1H)NOESY
NMR detailsText: sturcture determined using combined triple resonance and 2D homonuclear techniques

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Sample preparation

DetailsContents: 1.2MM XPF U-15N,13C; 10mM phosphate; 400mM sodium chloride; 92 % h2o, 8% d2o
Solvent system: 92% H2O, 8% D2O
Sample conditionsIonic strength: 400mM NaCl / pH: 5 / Pressure: 1 atm / Temperature: 293.6 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5brukercollection
NMRPipe2.3f. delaglioprocessing
CYANA2P. guntertstructure solution
Sparky3.11T.D. Goddard and D.G. Knellerdata analysis
CNSA. brungerrefinement
RefinementMethod: torsion angle dynamics; simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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