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- PDB-5e50: APLF/XRCC4 complex -

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Basic information

Entry
Database: PDB / ID: 5.0E+50
TitleAPLF/XRCC4 complex
Components
  • Aprataxin and PNK-like factor
  • XRCC4
KeywordsLYASE / FHA domain / APLF / XRCC4 / complex
Function / homology
Function and homology information


FHA domain binding / ADP-D-ribose modification-dependent protein binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / regulation of isotype switching / histone chaperone activity / poly-ADP-D-ribose binding / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition ...FHA domain binding / ADP-D-ribose modification-dependent protein binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / regulation of isotype switching / histone chaperone activity / poly-ADP-D-ribose binding / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / DNA repair-dependent chromatin remodeling / cellular response to lithium ion / 2-LTR circle formation / site of DNA damage / response to X-ray / SUMOylation of DNA damage response and repair proteins / protein folding chaperone / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / embryo implantation / DNA endonuclease activity / Nonhomologous End-Joining (NHEJ) / 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 / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / PNK, FHA domain / FHA domain / XRCC4-like, N-terminal domain superfamily / Tumour Suppressor Smad4 - #20 ...Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / PNK, FHA domain / FHA domain / XRCC4-like, N-terminal domain superfamily / Tumour Suppressor Smad4 - #20 / DNA repair protein XRCC4-like, C-terminal / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA repair protein XRCC4 / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.376 Å
AuthorsCherry, A.L. / Smerdon, S.J.
CitationJournal: DNA Repair (Amst.) / Year: 2015
Title: Versatility in phospho-dependent molecular recognition of the XRCC1 and XRCC4 DNA-damage scaffolds by aprataxin-family FHA domains.
Authors: Cherry, A.L. / Nott, T.J. / Kelly, G. / Rulten, S.L. / Caldecott, K.W. / Smerdon, S.J.
History
DepositionOct 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aprataxin and PNK-like factor
B: Aprataxin and PNK-like factor
C: XRCC4
D: XRCC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6596
Polymers26,6104
Non-polymers492
Water7,242402
1
A: Aprataxin and PNK-like factor
D: XRCC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3293
Polymers13,3052
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-6 kcal/mol
Surface area7160 Å2
MethodPISA
2
B: Aprataxin and PNK-like factor
C: XRCC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3293
Polymers13,3052
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-5 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.496, 58.540, 94.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 12087.028 Da / Num. of mol.: 2
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: Protein/peptide XRCC4


Mass: 1217.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13426*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein complex at 10 mg/ml, in 50 mM HEPES pH 7.5, 150 mM NaCl, 5 mM beta-mercaptoethanol. The complex crystallised from hanging drops set up at 18 oC with equal volumes of protein and ...Details: Protein complex at 10 mg/ml, in 50 mM HEPES pH 7.5, 150 mM NaCl, 5 mM beta-mercaptoethanol. The complex crystallised from hanging drops set up at 18 oC with equal volumes of protein and reservoir solution 0.1M Tris pH 8.0, 30% w/v PEG 3350, 0.2M MgCl2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9805 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. obs: 45157 / % possible obs: 98 % / Redundancy: 6.5 % / Net I/σ(I): 26.7
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.376→27.971 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 14.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1737 2210 5.03 %random
Rwork0.1365 ---
obs0.1384 43936 96.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.866 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0382 Å2-0 Å20 Å2
2---3.8507 Å20 Å2
3---1.8125 Å2
Refinement stepCycle: LAST / Resolution: 1.376→27.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 2 402 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111944
X-RAY DIFFRACTIONf_angle_d1.362640
X-RAY DIFFRACTIONf_dihedral_angle_d18.42753
X-RAY DIFFRACTIONf_chiral_restr0.092280
X-RAY DIFFRACTIONf_plane_restr0.007349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3757-1.40560.2111110.14542291X-RAY DIFFRACTION87
1.4056-1.43830.19821420.13192470X-RAY DIFFRACTION93
1.4383-1.47430.17961170.12342501X-RAY DIFFRACTION94
1.4743-1.51410.18071510.11422514X-RAY DIFFRACTION96
1.5141-1.55870.17931220.11242583X-RAY DIFFRACTION96
1.5587-1.6090.15671380.09942570X-RAY DIFFRACTION97
1.609-1.66650.13811310.10212613X-RAY DIFFRACTION97
1.6665-1.73320.14651430.10042601X-RAY DIFFRACTION98
1.7332-1.81210.15211580.1052604X-RAY DIFFRACTION98
1.8121-1.90760.1721280.1112655X-RAY DIFFRACTION99
1.9076-2.02710.14071500.10672684X-RAY DIFFRACTION99
2.0271-2.18350.15281530.11492666X-RAY DIFFRACTION99
2.1835-2.40320.18121470.13282684X-RAY DIFFRACTION99
2.4032-2.75060.17951450.15772715X-RAY DIFFRACTION100
2.7506-3.46450.18631280.14462772X-RAY DIFFRACTION100
3.4645-27.97640.17651460.15662803X-RAY DIFFRACTION97

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