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- PDB-6tyu: Structure of Ku80 von Willebrand domain complexed with MRI Ku Bin... -

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Basic information

Entry
Database: PDB / ID: 6tyu
TitleStructure of Ku80 von Willebrand domain complexed with MRI Ku Binding Motif
Components
  • LYS-THR-ARG-VAL-LEU-PRO-SER-TRP-LEU-THR-ALA
  • 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


negative regulation of double-strand break repair via nonhomologous end joining / Ku70:Ku80 complex / telomeric DNA binding / DNA helicase activity / telomere maintenance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / DNA recombination / damaged DNA binding / hydrolase activity ...negative regulation of double-strand break repair via nonhomologous end joining / Ku70:Ku80 complex / telomeric DNA binding / DNA helicase activity / telomere maintenance / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / DNA recombination / damaged DNA binding / hydrolase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Modulator of retrovirus infection / Modulator of retrovirus infection / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm ...Modulator of retrovirus infection / Modulator of retrovirus infection / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 N-terminal alpha/beta 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 / 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 / Cell cycle regulator of non-homologous end joining
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.46862727205 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

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Assembly

Deposited unit
A: X-ray repair cross-complementing protein 5
B: LYS-THR-ARG-VAL-LEU-PRO-SER-TRP-LEU-THR-ALA


Theoretical massNumber of molelcules
Total (without water)28,0042
Polymers28,0042
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-4 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.574, 71.350, 79.163
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: 26185.980 Da / Num. of mol.: 1 / Fragment: Ku80 von Willebrand domain / Mutation: C190S, deletion loop (E171 through R188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: xrcc5, xrcc5-A-prov / 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 LYS-THR-ARG-VAL-LEU-PRO-SER-TRP-LEU-THR-ALA


Mass: 1818.078 Da / Num. of mol.: 1 / Fragment: MRI Ku Binding Motif / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BWK5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium formate, 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: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.468→50 Å / Num. obs: 43410 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 19.8245300615 Å2 / Rrim(I) all: 0.048 / Net I/σ(I): 53
Reflection shellResolution: 1.47→1.5 Å / Num. unique obs: 1900 / Rrim(I) all: 0.602

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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: 6TYV

6tyv


Resolution: 1.46862727205→37.8033786401 Å / SU ML: 0.149935107514 / Cross valid method: FREE R-VALUE / σ(F): 1.33538037603 / Phase error: 22.8412027977
RfactorNum. reflection% reflection
Rfree0.200770793241 2152 5.00092954081 %
Rwork0.178048002916 --
obs0.179161282252 43032 98.1793292266 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.8655062593 Å2
Refinement stepCycle: LAST / Resolution: 1.46862727205→37.8033786401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 0 192 1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008096096415841800
X-RAY DIFFRACTIONf_angle_d0.9050796324992452
X-RAY DIFFRACTIONf_chiral_restr0.0710383971692290
X-RAY DIFFRACTIONf_plane_restr0.00519177204981320
X-RAY DIFFRACTIONf_dihedral_angle_d12.8439504643660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4687-1.50280.3108422021381240.2667769692362394X-RAY DIFFRACTION87.4913134121
1.5028-1.54040.2394041332621430.2248212932422711X-RAY DIFFRACTION98.4137931034
1.5404-1.5820.2461755473061410.2201939352382684X-RAY DIFFRACTION98.8453463961
1.582-1.62860.2059628929081410.2077546321922711X-RAY DIFFRACTION99.3728222997
1.6286-1.68110.2632583258991470.2014952442972750X-RAY DIFFRACTION99.9310106933
1.6811-1.74120.2662009066491430.2104636572442723X-RAY DIFFRACTION99.2726013162
1.7412-1.81090.2461632774041420.2232519497822721X-RAY DIFFRACTION98.9288182446
1.8109-1.89340.2859279049291420.2172131731472658X-RAY DIFFRACTION96.6183574879
1.8934-1.99320.2242494612241410.1996894993712720X-RAY DIFFRACTION98.3499484359
1.9932-2.1180.2014202972691480.1737513598852748X-RAY DIFFRACTION99.8276456394
2.118-2.28160.175634811171450.1687816619842766X-RAY DIFFRACTION99.6917808219
2.2816-2.51110.208205500511430.1671128641372752X-RAY DIFFRACTION98.7043982271
2.5111-2.87440.1660992017081470.1687361924352753X-RAY DIFFRACTION97.9398851739
2.8744-3.6210.1973999195031460.1709662084512830X-RAY DIFFRACTION99.3987975952
3.621-37.8030.1835325958351590.1634446742692959X-RAY DIFFRACTION99.7440818938
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)
10.6273965993730.121969398122-0.1353704260970.4307919588350.1822344073431.36313695226-0.009405414470060.08729497399870.0375698562062-0.4899496818220.00599787895853-0.079865533894-0.0229199353249-0.05585404675560.004922048009490.211759548340.01035021632390.03170463221660.190597306195-0.009986326078910.1885071603723.075291688026.8134803424212.9064399156
20.4915534166940.1068458293120.006996254565740.7800741838070.3962104964620.505204156463-0.140058092280.1683439625840.0249787826206-0.4121894352060.0074122201901-0.08821064271450.0874661630316-0.0830571484234-0.1978738307520.2992220396815.06152012808E-50.09006419012250.2316175530170.006436952608890.2217123092797.546005511872.388332975655.38904328479
30.1547160577780.00190437369063-0.1769015288170.948097041499-0.09299895432611.06200559852-0.1076335595580.19104820121-0.213245244028-0.820069275802-0.119335904353-0.4270837247170.4688214475070.192184034542-0.09533601565460.3634034954540.05471124130740.190525753380.19891879260.01546551566150.2629191392628.76719067192-7.1941844595810.80632149
41.409834502660.2715665930931.070804171092.11516388361-0.1405456051270.852686465325-0.125976617064-0.1103430786380.052299759321-0.3148630680410.1699943936670.4779866581680.199103833652-0.3186928278320.04647831181480.149745228089-0.0237700497275-0.006927426617530.1861027907680.001696017159250.214374457556-5.5899568561-4.5928534805320.5351452644
51.534428069220.551618794066-1.627412336994.50115287452-0.4786222958221.74213224628-0.6134018403850.970027635556-0.124761644945-1.302317064960.2524035946170.541364368340.685112957932-0.760345788061-1.479603039360.590654971807-0.1594773724640.02027954263120.4456361165030.02696143995610.234440246693.03606700883-7.983743335085.30864738636
61.519589598371.2728067951-0.6073615937542.08788723631-0.7103170050891.86475843503-0.2056913058-0.107635409416-0.0713408001931-0.1905277649010.09429496704-0.2937972170550.203750253239-0.00776593382296-0.07744532798980.144592901166-0.003213460881990.03054053799030.140940178918-0.01644983063280.1617563302214.93771932195-5.2874922789419.8924986929
70.1844997381720.4352897375280.04578468803871.41212874580.1805164582032.304891093370.00907242789336-0.07404650724690.01013682196790.162849552517-0.0085819941343-0.3338232149990.2109882890270.1573385958960.004778752555960.1220194366690.0252259061292-0.03449653113430.201576531150.008757967600920.2189965896488.234031948991.2757867511927.670887319
80.00176045656820.07418583785420.04062349827050.6108877553020.3507144247870.378856391593-0.2455428144350.03187683967070.07398397339940.07057019308820.271445937472-0.475360656311-0.2458093351060.2614773955320.006205594252110.196930440741-0.00827070855823-0.0172191320640.237607123262-0.01495011542470.31024994405610.14415608518.962578496719.4411843773
90.416038384899-0.4845284228230.7765122491680.583913762951-0.8942087560081.420353920920.0149597876295-0.230221075572-0.1307036826570.695542708405-0.0420677960551-0.538029418149-0.2104968891880.3488018874310.007461138904310.2396524739530.00229021989792-0.1341070826070.2491752964730.02930933455430.36073972705313.19934537079.5982086751428.8530115294
100.03035304307770.0444544133447-0.0899265123920.295381804453-0.04268141370310.280087494287-0.0869353254306-0.179066868643-0.110759157254-0.357103347949-0.0709660622315-0.7249522109830.2054548035580.902205031930.002396604874830.353718992194-0.01820852406120.05936977258890.4879048786780.05103104527040.46118073928616.01540165156.5042069594413.2737492381
110.04932499229850.0149569992457-0.03556596993130.152540505322-0.02910773555070.04637852100180.0784313563577-0.1902862154680.0968284225610.724522093501-0.08076037435270.179319382050.235281346214-0.227449430891-0.001027904847310.222119511801-0.0178746637172-0.01011902923230.2109102813240.01252541188560.1994187849432.65390019637-10.769819048732.526164779
122.37714696306-1.144118648681.531630851476.195839960891.527760003042.54599763872-0.284255076708-0.2109522747510.2725191159590.1592452197240.461465028207-0.478479022856-0.272677913770.02846801412470.1365811922510.588195480370.0133997402265-0.1848960875290.407327247397-0.09776690907190.3014547958655.74006438323-12.92950458437.3130320653
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 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 58 )
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 95 )
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 163 )
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 197 )
9X-RAY DIFFRACTION9chain 'A' and (resid 198 through 221 )
10X-RAY DIFFRACTION10chain 'A' and (resid 222 through 235 )
11X-RAY DIFFRACTION11chain 'B' and (resid 12 through 17 )
12X-RAY DIFFRACTION12chain 'B' and (resid 18 through 19 )

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