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- PDB-2lyh: Structure of Faap24 residues 141-215 -

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Basic information

Entry
Database: PDB / ID: 2lyh
TitleStructure of Faap24 residues 141-215
ComponentsFanconi anemia-associated protein of 24 kDa
KeywordsDNA BINDING PROTEIN / interstrand crosslink repair / Fanconi anemia
Function / homology
Function and homology information


FANCM-MHF complex / Fanconi anaemia nuclear complex / interstrand cross-link repair / Fanconi Anemia Pathway / PKR-mediated signaling / intracellular membrane-bounded organelle / chromatin binding / chromatin / DNA binding / nucleoplasm / cytosol
Similarity search - Function
Fanconi anemia-associated protein of 24kDa / Fanconi anemia core complex-associated protein 24, pseudonuclease domain / FANCM pseudonuclease domain / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / RuvA domain 2-like / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fanconi anemia core complex-associated protein 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWienk, H. / Slootweg, J. / Kaptein, R. / Boelens, R. / Folkers, G.E.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition.
Authors: Wienk, H. / Slootweg, J.C. / Speerstra, S. / Kaptein, R. / Boelens, R. / Folkers, G.E.
History
DepositionSep 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fanconi anemia-associated protein of 24 kDa


Theoretical massNumber of molelcules
Total (without water)10,7501
Polymers10,7501
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Fanconi anemia-associated protein of 24 kDa


Mass: 10750.467 Da / Num. of mol.: 1 / Fragment: UNP residues 141-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C19orf40, FAAP24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9BTP7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.2 mM [U-100% 13C; U-100% 15N] FAAP24, 50 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM PMSF, 8 % D2O, 92 % H2O, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMFAAP24-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
0.2 mMPMSF-41
8 %D2O-51
92 %H2O-61
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
WHAT IFVrienddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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