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- PDB-2kp7: Solution NMR structure of the Mus81 N-terminal HhH. Northeast Str... -

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Basic information

Entry
Database: PDB / ID: 2kp7
TitleSolution NMR structure of the Mus81 N-terminal HhH. Northeast Structural Genomics Consortium target MmT1A
ComponentsCrossover junction endonuclease MUS81
KeywordsHYDROLASE / Helix-hairpin-Helix / tumour suppressor / DNA damage / DNA recombination / DNA repair / Endonuclease / Magnesium / Metal-binding / Nuclease / Nucleus / Phosphoprotein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Fanconi Anemia Pathway / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / osteoblast proliferation / Holliday junction resolvase complex / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication ...: / Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Fanconi Anemia Pathway / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / osteoblast proliferation / Holliday junction resolvase complex / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication / mitotic intra-S DNA damage checkpoint signaling / DNA repair / nucleolus / DNA binding / nucleus / metal ion binding
Similarity search - Function
ERCC4 domain / ERCC4 domain / ERCC4 domain / Restriction endonuclease type II-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase lambda lyase domain superfamily / DNA polymerase; domain 1 / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Crossover junction endonuclease MUS81
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLaister, R.C. / Wu, B. / Lemak, A. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure and DNA binding mode of the Mus81 n-terminal helix-hairpin-helix domain
Authors: Laister, R.C. / Duan, S. / Wu, B. / Herzanych, N. / Montelione, G.T. / Arrowsmith, C.H.
History
DepositionOct 7, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crossover junction endonuclease MUS81


Theoretical massNumber of molelcules
Total (without water)10,1311
Polymers10,1311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Crossover junction endonuclease MUS81


Mass: 10130.780 Da / Num. of mol.: 1 / Fragment: sequence database residues 11-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mus81 / Production host: Escherichia coli (E. coli)
References: UniProt: Q91ZJ0, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D C(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D 1H-15N NOESY
1823D CCH-TOCSY
1923D HCH-TOCSY
11023D 1H-13C NOESY
11123D 1H-13C NOESY aro
1122CB-HD
1132CB-HE

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] Mus81 NTD, 25 mM sodium phosphate, 500 mM sodium chloride, 2 mM DTT, 2 mM benzamidine, 0.5 mM PMSF, 0.5 mM EDTA, 0.5 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Mus81 NTD, 25 mM sodium phosphate, 500 mM sodium chloride, 2 mM benzamidine, 2 mM DTT, 0.5 mM EDTA, 0.5 mM PMSF, 0.5 mM TCEP, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMus81 NTD-1[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-21
500 mMsodium chloride-31
2 mMDTT-41
2 mMbenzamidine-51
0.5 mMPMSF-61
0.5 mMEDTA-71
0.5 mMTCEP-81
1 mMMus81 NTD-9[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-102
500 mMsodium chloride-112
2 mMbenzamidine-122
2 mMDTT-132
0.5 mMEDTA-142
0.5 mMPMSF-152
0.5 mMTCEP-162
Sample conditionsIonic strength: 500 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AvanceBrukerAVANCE8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas and Arrowsmithprocessing
XEASYBartels et al.chemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVSBhattacharya and Montelionenmr structure quality assessment
RefinementMethod: 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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