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- PDB-2kqb: First PBZ domain of human APLF protein -

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Basic information

Entry
Database: PDB / ID: 2kqb
TitleFirst PBZ domain of human APLF protein
ComponentsAprataxin and PNK-like factor
KeywordsLYASE / ADP-ribosylation / DNA damage / DNA repair / Metal-binding / Nucleotide-binding / Nucleus / Zinc / Zinc-finger
Function / homology
Function and homology information


ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / protein localization to chromatin / 3'-5' exonuclease activity ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / protein localization to chromatin / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / embryo implantation / protein folding chaperone / DNA endonuclease activity / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / histone binding / Hydrolases; Acting on ester bonds / DNA repair / nucleotide binding / DNA damage response / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsNeuhaus, D. / Eustermann, S. / Brockmann, C. / Yang, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose).
Authors: Eustermann, S. / Brockmann, C. / Mehrotra, P.V. / Yang, J.C. / Loakes, D. / West, S.C. / Ahel, I. / Neuhaus, D.
History
DepositionNov 4, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 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: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aprataxin and PNK-like factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1182
Polymers10,0531
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aprataxin and PNK-like factor / Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1- ...Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1-interacting protein 1


Mass: 10053.062 Da / Num. of mol.: 1
Fragment: sequence database residues 363-451, PBZ-type 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLF, C2orf13, PALF, XIP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IW19, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Compound detailsRESIDUES 418-451 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE CALCULATIONS WERE CARRIED OUT ...RESIDUES 418-451 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE CALCULATIONS WERE CARRIED OUT ON RESIDUES 363-417 ONLY.

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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-15N HMQC long-range
1312D 1H-13C HSQC full-width
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic
1612D 1H-1H NOESY
1712D 1H-1H NOESY filtered
1813D CBCANH
1913D CBCA(CO)NH
11013D HBHANH
11113D HBHA(CO)NH
11213D (H)CCH-TOCSY
11313D (H)CCH-TOCSY
11413D 1H-15N NOESY
11513D 1H-13C NOESY
11613D HNHB
11723D HACAHB-COSY
NMR detailsText: The author states that NMR was carried out on a single fragment (363-451) containing both fingers F1 and F2 of APLF, but the structure calculations were carried out separately for each finger. ...Text: The author states that NMR was carried out on a single fragment (363-451) containing both fingers F1 and F2 of APLF, but the structure calculations were carried out separately for each finger. This co-ordinate file includes residues 363-417 and contains F1 as well as the unstructured regions on either side.

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.5-0.6 mM [U-98% 13C; U-98% 15N] APLF_363-451, 95% H2O/5% D2O95% H2O/5% D2O
220 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.5-0.6 mM [U-98% 13C; U-98% 15N] APLF_363-451, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMpotassium pyrophosphate-11
200 mMsodium chloride-21
100 uMzinc sulphate-31
2 mMDTT-4[U-2H]1
mMAPLF_363-451-5[U-98% 13C; U-98% 15N]0.5-0.61
20 mMpotassium pyrophosphate-62
200 mMsodium chloride-72
100 uMzinc sulphate-82
2 mMDTT-9[U-2H]2
mMAPLF_363-451-10[U-98% 13C; U-98% 15N]0.5-0.62
Sample conditionsIonic strength: 0.4 / pH: 6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameDeveloperClassification
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddardchemical shift assignment
CCPN_analysisCCPNchemical shift assignment
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 11 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 12 / Protein psi angle constraints total count: 13
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25 / Maximum torsion angle constraint violation: 6.5 ° / Maximum upper distance constraint violation: 0.57 Å / Torsion angle constraint violation method: XPLOR-NIH

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