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- PDB-2k2w: Second BRCT domain of NBS1 -

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Basic information

Entry
Database: PDB / ID: 2k2w
TitleSecond BRCT domain of NBS1
ComponentsRecombination and DNA repair protein
KeywordsCELL CYCLE / BRCT domain / DNA repair / Cell cycle checkpoint
Function / homology
Function and homology information


mitotic cell cycle checkpoint signaling / Mre11 complex / regulation of fibroblast proliferation / : / nuclear inclusion body / isotype switching / mitotic G2 DNA damage checkpoint signaling / transcription factor binding / telomere maintenance / meiotic cell cycle ...mitotic cell cycle checkpoint signaling / Mre11 complex / regulation of fibroblast proliferation / : / nuclear inclusion body / isotype switching / mitotic G2 DNA damage checkpoint signaling / transcription factor binding / telomere maintenance / meiotic cell cycle / double-strand break repair / chromosome, telomeric region
Similarity search - Function
Nibrin, BRCT2 domain / Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Nibrin-related / Forkhead associated domain ...Nibrin, BRCT2 domain / Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Nibrin-related / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing
AuthorsXu, C. / Cui, G. / Botuyan, M. / Mer, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of a second BRCT domain identified in the nijmegen breakage syndrome protein Nbs1 and its function in an MDC1-dependent localization of Nbs1 to DNA damage sites.
Authors: Xu, C. / Wu, L. / Cui, G. / Botuyan, M.V. / Chen, J. / Mer, G.
History
DepositionApr 14, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 29, 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: Recombination and DNA repair protein


Theoretical massNumber of molelcules
Total (without water)13,2371
Polymers13,2371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Recombination and DNA repair protein


Mass: 13237.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: NBS1 / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6EKW1, UniProt: Q6XV80*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HBHA(CO)NH
1623D HNCO
1723D HCACO
1823D H(CCO)NH
1923D C(CO)NH
11023D HN(CA)CB
11123D (H)CCH-COSY
11223D CCH-COSY
11323D CCH-TOCSY
11413D 1H-15N NOESY
11513D 1H-15N TOCSY
11623D 1H-13C NOESY aliphatic
11722D (HB)CB(CGCD)HD
11823D 1H-13C AROMATIC

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 50 mM sodium chloride, 50 mM glutamic acid, 50 mM arginine, 0.3-0.5 mM [U-100% 15N] protein, 93% H2O/7% D2O93% H2O/7% D2O
220 mM sodium phosphate, 50 mM sodium chloride, 50 mM glutamic acid, 50 mM arginine, 0.3-0.5 mM [U-100% 13C; U-100% 15N] protein, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate1
50 mMsodium chloride1
50 mMglutamic acid1
50 mMarginine1
0.3 mMentity[U-100% 15N]1
20 mMsodium phosphate2
50 mMsodium chloride2
50 mMglutamic acid2
50 mMarginine2
0.3 mMentity[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.1 / pH: 6.7 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
TALOSWishartdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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