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- PDB-5w7w: Crystal Structure of FHA domain of human APLF -

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Basic information

Entry
Database: PDB / ID: 5w7w
TitleCrystal Structure of FHA domain of human APLF
ComponentsAprataxin and PNK-like factor
KeywordsPROTEIN BINDING / scaffold protein / DNA repair / NHEJ
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 / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / DNA-(apurinic or apyrimidinic site) endonuclease activity ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / DNA-(apurinic or apyrimidinic site) endonuclease activity / protein localization to chromatin / protein folding chaperone / 3'-5' exonuclease activity / embryo implantation / 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 / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.348 Å
AuthorsPedersen, L.C. / Kim, K. / London, R.E.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Characterization of the APLF FHA-XRCC1 phosphopeptide interaction and its structural and functional implications.
Authors: Kim, K. / Pedersen, L.C. / Kirby, T.W. / DeRose, E.F. / London, R.E.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,0517
Polymers23,8442
Non-polymers2075
Water6,017334
1
T: Aprataxin and PNK-like factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0604
Polymers11,9221
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aprataxin and PNK-like factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9913
Polymers11,9221
Non-polymers692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.794, 96.944, 34.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

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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: 11921.815 Da / Num. of mol.: 2 / Fragment: UNP residues 1-105
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.348→25.267 Å / Num. obs: 41939 / % possible obs: 97.2 % / Redundancy: 7 % / Rpim(I) all: 0.027 / Rsym value: 0.088 / Net I/σ(I): 24.8
Reflection shellResolution: 1.348→1.37 Å / Redundancy: 1.8 % / Num. unique obs: 1696 / Rpim(I) all: 0.245 / Rsym value: 0.29 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BRF

2brf


Resolution: 1.348→25.267 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 16.19
RfactorNum. reflection% reflectionSelection details
Rfree0.1642 1937 4.64 %random
Rwork0.1472 ---
obs0.148 41769 96.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.348→25.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 13 334 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071726
X-RAY DIFFRACTIONf_angle_d0.9442348
X-RAY DIFFRACTIONf_dihedral_angle_d15.499657
X-RAY DIFFRACTIONf_chiral_restr0.082254
X-RAY DIFFRACTIONf_plane_restr0.008313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3484-1.38210.24971090.21822275X-RAY DIFFRACTION78
1.3821-1.41950.21291290.18992681X-RAY DIFFRACTION93
1.4195-1.46120.19551370.16782699X-RAY DIFFRACTION94
1.4612-1.50840.18191360.1552804X-RAY DIFFRACTION96
1.5084-1.56230.19111360.15072798X-RAY DIFFRACTION97
1.5623-1.62480.16681350.14762849X-RAY DIFFRACTION98
1.6248-1.69880.16731410.14932896X-RAY DIFFRACTION100
1.6988-1.78830.18671420.15562915X-RAY DIFFRACTION100
1.7883-1.90030.18781430.14622927X-RAY DIFFRACTION100
1.9003-2.0470.15871430.13272934X-RAY DIFFRACTION100
2.047-2.25280.15821420.13162941X-RAY DIFFRACTION100
2.2528-2.57860.17221440.14842963X-RAY DIFFRACTION100
2.5786-3.24760.17241460.14992995X-RAY DIFFRACTION100
3.2476-25.27170.13431540.14373155X-RAY DIFFRACTION100

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