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- PDB-6tyw: Structure of Ku80 von Willebrand domain S229A mutant complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6tyw
TitleStructure of Ku80 von Willebrand domain S229A mutant complexed with APLF Ku Binding Motif
Components
  • GLU-ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA-GLU
  • X-ray repair cross-complementing protein 5
KeywordsDNA BINDING PROTEIN / Ku80 von Willebrand factor A domain / Fluorine-19 NMR / Ku binding motif / Conditional binding site
Function / homology
Function and homology information


ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / Ku70:Ku80 complex / poly-ADP-D-ribose binding / histone chaperone activity / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / telomeric DNA binding / site of DNA damage ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / Ku70:Ku80 complex / poly-ADP-D-ribose binding / histone chaperone activity / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / telomeric DNA binding / site of DNA damage / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / embryo implantation / protein folding chaperone / DNA helicase activity / telomere maintenance / DNA endonuclease activity / double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair / site of double-strand break / DNA recombination / histone binding / damaged DNA binding / Hydrolases; Acting on ester bonds / hydrolase activity / DNA repair / nucleotide binding / DNA damage response / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm ...Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / von Willebrand factor, type A domain / SMAD/FHA domain superfamily / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
X-ray repair cross-complementing protein 5 / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69965540409 Å
AuthorsMin, J. / Pedersen, L.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA-ES102645 United States
CitationJournal: DNA Repair (Amst.) / Year: 2019
Title: Ligand binding characteristics of the Ku80 von Willebrand domain.
Authors: Kim, K. / Min, J. / Kirby, T.W. / Gabel, S.A. / Pedersen, L.C. / London, R.E.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: X-ray repair cross-complementing protein 5
B: GLU-ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2003
Polymers28,1382
Non-polymers621
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint0 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.847, 71.383, 79.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein X-ray repair cross-complementing protein 5


Mass: 26169.980 Da / Num. of mol.: 1 / Fragment: Ku80 von Willebrand domain / Mutation: C190S, S229A, deletion loop (E171 through R188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18044412mg / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1L8EVE5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein/peptide GLU-ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA-GLU


Mass: 1968.368 Da / Num. of mol.: 1 / Fragment: APLF Ku Binding Motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IW19*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.699→50 Å / Num. obs: 28054 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 20.1101330671 Å2 / Rrim(I) all: 0.057 / Net I/σ(I): 50.6
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1191 / Rrim(I) all: 0.156

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TYZ

6tyz


Resolution: 1.69965540409→22.8064946926 Å / SU ML: 0.150952043558 / Cross valid method: FREE R-VALUE / σ(F): 1.33572853688 / Phase error: 25.3720659353
RfactorNum. reflection% reflection
Rfree0.21816164121 1399 5.01343845189 %
Rwork0.179346577365 --
obs0.181250894086 27905 98.5346045198 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.0836204142 Å2
Refinement stepCycle: LAST / Resolution: 1.69965540409→22.8064946926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 4 219 1992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00867034443621878
X-RAY DIFFRACTIONf_angle_d0.9135625764382544
X-RAY DIFFRACTIONf_chiral_restr0.0596734920045293
X-RAY DIFFRACTIONf_plane_restr0.00566523393755332
X-RAY DIFFRACTIONf_dihedral_angle_d12.8512208296691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6997-1.76040.2912158470751230.2200661926412371X-RAY DIFFRACTION90.3623188406
1.7604-1.83080.2298881801881460.2117008874982634X-RAY DIFFRACTION99.1087344029
1.8308-1.91410.2373861131661340.197818746052632X-RAY DIFFRACTION99.6038890889
1.9141-2.0150.2657510302771390.1968344942792652X-RAY DIFFRACTION99.6785714286
2.015-2.14110.233254802721420.1892818543642653X-RAY DIFFRACTION99.7145915091
2.1411-2.30630.2276741330511420.1860891383472674X-RAY DIFFRACTION99.3648553282
2.3063-2.53810.2817673222081360.1836886007792650X-RAY DIFFRACTION99.1812032752
2.5381-2.90480.2114839835821430.1846453867672674X-RAY DIFFRACTION99.0158172232
2.9048-3.65730.1919706976921420.1738555246132722X-RAY DIFFRACTION99.5135510771
3.6573-22.80640.1941304923991520.1619757730892844X-RAY DIFFRACTION99.6341868972
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.341131762044.12185521251-0.1588898084556.967700146260.9534386034541.67805404873-0.0105453464919-0.07376795953250.01136713158270.404298409878-0.03883165959780.0719041101212-0.008952253311430.05402001573380.02889605400020.1690122072710.002524401926650.01752393567260.1817892881630.01792956963770.182377983039-3.182810887916.99295110369-13.3011182347
21.0660830732-0.345576278458-0.9340967076491.24159522431-0.2130714383011.69512329546-0.297203005891-0.109491605955-0.176077976720.4030939202580.06933318157290.159257973210.422668590746-0.113519843603-0.05632889167360.262601436334-0.01142874951680.08336047676310.1918962261980.0005289115286130.199150058957-8.59321072237-1.27801318799-7.82404355533
33.711449486130.2380152041611.138874561085.1281503634-0.6716255038281.60877160745-0.07166281284960.05563668251860.04793495600990.2526448666110.117002011655-0.56753726610.1740353505780.3441788772590.02406092890290.1552209579140.0306364033287-0.003636175477340.175781795279-0.006703792087210.2217661193725.71728546683-4.6481559597-20.9119468998
41.24995358457-0.285758113531-1.011882045064.118670582832.928849060513.47116562945-0.384489632657-0.781782101596-0.312250687881.056225121630.217575559343-0.3656797526761.37924631130.4644107559520.2111173002380.5195605120720.1969003074460.06485276167070.5133665188850.04045232212160.289119532384-3.68019358513-8.31634210424-5.46572510759
51.78110967764-0.941383101851-0.32503156842.217326362310.9838523242472.15750958881-0.1448103625480.0391120996452-0.02679884418020.293231854951-0.008776190289640.3891181426340.313082065561-0.07025578594320.01800332078580.177749894695-0.01072905003230.05684911395390.1671340908720.0003668656709660.181115640091-5.51643396882-5.15186066061-20.8870849383
60.372935055789-0.236941541004-0.1124395263512.380564136220.5930147626013.41800246084-0.04739853285780.04018525053690.0166073279029-0.1342781658760.01970793356130.4057442782340.0634078012196-0.109056404670.03102842367850.1181259341240.000918705943125-0.03347573532290.213380413730.0007602342001240.259288584696-8.587535362090.751274068-28.1872350784
74.248251774611.57350847084-0.5197458924385.44635542125-2.121286826852.414810178650.1462731352080.05379466512650.5107581648020.2113698130470.2660262214970.951929485988-0.194330397421-0.668175667362-0.4243088291680.2988900839330.0209499876277-0.005378834032340.2869881431790.03834122184150.363884937404-11.477231067920.6674287598-20.098707624
81.3755963434-1.052922934440.9277031204642.672843296831.847897461393.18825228739-0.117884526964-0.144682091267-0.2790654998490.0365796878773-0.1423938302830.6808281620760.221255433792-0.4907508967080.1657048555850.2353905153030.00185575371536-0.03283207627960.295721060844-0.02334884258050.383458945222-15.46487440075.89988549669-23.1121042625
99.058241039444.66482896083-1.430153085296.243438588150.8127322523985.259810646760.342195013750.0373280710760.118952383458-0.301735893986-0.175611831645-0.340571921055-0.303570918980.119832143198-0.1584503188510.1906446571950.02904064808770.04886980773030.2129060938720.02348675957050.1708357673512.37356072531-2.29117145117-34.8958469592
106.187233401282.65345230458-0.6091692562311.8326125331-2.105093392287.826302797170.002873657066820.502042744022-0.394049284921-0.87462511614-0.1260812957250.4790424572390.246456911041-0.5608144176050.0788312849140.2725096620640.021619366798-0.05662071838740.250647660488-0.0697172832880.24103435146-5.33729004023-12.8678941683-34.6927799209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 134 )
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 241 )
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 187 )
10X-RAY DIFFRACTION10chain 'B' and (resid 188 through 193 )

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