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

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Basic information

Entry
Database: PDB / ID: 6tyx
TitleStructure of Ku80 von Willebrand domain S229A mutant complexed with XLF Ku Binding Motif
Components
  • LYS-GLY-LEU-PHE-MET
  • 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


DNA ligase IV complex / Ku70:Ku80 complex / DNA end binding / telomeric DNA binding / telomere maintenance / DNA helicase activity / double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / damaged DNA binding ...DNA ligase IV complex / Ku70:Ku80 complex / DNA end binding / telomeric DNA binding / telomere maintenance / DNA helicase activity / double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / damaged DNA binding / hydrolase activity / ATP binding
Similarity search - Function
XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / XRCC4-like, N-terminal domain superfamily / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 ...XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / XRCC4-like, N-terminal domain superfamily / 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 / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-homologous end-joining factor 1 / X-ray repair cross-complementing protein 5
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89944353227 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: X-ray repair cross-complementing protein 5
C: LYS-GLY-LEU-PHE-MET
D: LYS-GLY-LEU-PHE-MET


Theoretical massNumber of molelcules
Total (without water)56,1774
Polymers56,1774
Non-polymers00
Water4,107228
1
A: X-ray repair cross-complementing protein 5
C: LYS-GLY-LEU-PHE-MET


Theoretical massNumber of molelcules
Total (without water)28,0882
Polymers28,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-7 kcal/mol
Surface area10210 Å2
MethodPISA
2
B: X-ray repair cross-complementing protein 5
D: LYS-GLY-LEU-PHE-MET


Theoretical massNumber of molelcules
Total (without water)28,0882
Polymers28,0882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.798, 71.605, 74.600
Angle α, β, γ (deg.)90.000, 98.309, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 26169.980 Da / Num. of mol.: 2 / Fragment: Ku80 von Willebrand / 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 LYS-GLY-LEU-PHE-MET


Mass: 1918.394 Da / Num. of mol.: 2 / Fragment: APLF Ku Binding Motif / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8ENT6*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES NaOH pH 7.5, 25 % (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 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 36348 / % possible obs: 98.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 29.7417965936 Å2 / Rrim(I) all: 0.05 / Net I/σ(I): 39.7
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1765 / Rrim(I) all: 0.335

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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: 1.89944353227→40.685646148 Å / SU ML: 0.214299439303 / Cross valid method: FREE R-VALUE / σ(F): 1.33619816583 / Phase error: 24.2090853008
Details: The model of the 6xHis-tag in Chain B is based on the best guess for the discontinuous electron density.
RfactorNum. reflection% reflection
Rfree0.225010419974 1813 4.99862145023 %
Rwork0.184601605569 --
obs0.186661278414 36270 98.2181542461 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.8112569487 Å2
Refinement stepCycle: LAST / Resolution: 1.89944353227→40.685646148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 228 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429897082233432
X-RAY DIFFRACTIONf_angle_d0.6471348768894654
X-RAY DIFFRACTIONf_chiral_restr0.0433272526973552
X-RAY DIFFRACTIONf_plane_restr0.00375229952194603
X-RAY DIFFRACTIONf_dihedral_angle_d13.32511407691200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8995-1.95080.276549917361320.2670970816842504X-RAY DIFFRACTION92.2646132307
1.9508-2.00820.2783818114531340.2455017291162545X-RAY DIFFRACTION95.6444127097
2.0082-2.0730.2840730746871370.2082920896292603X-RAY DIFFRACTION97.439544808
2.073-2.14710.2200723132431390.2055541851392640X-RAY DIFFRACTION98.1285310734
2.1471-2.23310.2649656323581400.1952989427982652X-RAY DIFFRACTION98.3098591549
2.2331-2.33470.226919716091390.2070981210452639X-RAY DIFFRACTION98.197242842
2.3347-2.45780.2411975377141410.1929222459672666X-RAY DIFFRACTION99.2574257426
2.4578-2.61170.2249452200661400.1975824622952672X-RAY DIFFRACTION99.7163120567
2.6117-2.81330.2565245173471420.2061067652922704X-RAY DIFFRACTION99.3715083799
2.8133-3.09640.2455222814461390.2113940712762657X-RAY DIFFRACTION99.1841078397
3.0964-3.54420.2216344721981420.1794077197572710X-RAY DIFFRACTION99.9649491763
3.5442-4.46440.1908115687281420.1513901898222716X-RAY DIFFRACTION99.8253580161
4.4644-40.68560.209364874371460.166645733742749X-RAY DIFFRACTION99.5872033024
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)
17.06743792966-3.16356716441-0.1590611653445.033355788410.1716893510223.64373233001-0.06326712257830.2235488560290.2295047096330.438495846597-0.208027429361-0.31513695626-0.419426903993-0.555564623539-0.0248176888190.2409433991830.0246752830285-0.004968605637890.1326471273320.00904182003850.2141521890412.54524299026.10794404986-0.865200964879
23.24623728593-0.280934156246-0.2673741184770.184995500933-0.06983933336920.07267738745290.1229720982270.173802949173-0.386213318141-0.0931679749946-0.0980350125559-0.1172967636310.6652592332390.2046318529310.07342504556030.4264248218750.03387756177360.002179121592380.125447131177-0.006134320456460.34295441094220.4187626271-13.1774541422-7.90025199645
37.14467221299-5.500485662592.345087232246.38752235008-2.290232753484.417553577430.104020102790.00908740271786-0.125515452428-0.2703824249630.03405335427630.1068533428540.187309316012-0.423947375382-0.02927621882220.203361287806-0.0123591790481-0.01003597203570.216565049692-0.02070717752070.2472737208318.79092337021-0.677318150303-9.27805936194
41.18357316521.44957475372-0.4157394515492.246726704470.6097326804743.09213795929-0.05818230880460.04983925927940.421792375447-0.234803545377-0.0763386879461-0.347177878297-0.436372056116-0.08260050840660.1082807472750.2949128705260.0181101520757-0.01462338302570.130999527427-0.01152439193970.32869354495718.37629654488.11649866157-4.01224118816
51.36957483662-0.0280320297574-0.1456334595162.753523283730.3678474215442.28641592654-0.0792125497508-0.02250535803010.1025433189980.07991207804410.0170847909719-0.361889537325-0.3012490274720.09544000067220.0670470198640.202248654384-0.00388594647072-0.003521317175710.09767619034270.01032135329720.3261295888220.38081379826.5326100292-3.93936015833
60.2442332268370.01489197061810.06308958393293.813743218650.4615486406172.17141703789-0.148206485487-0.2139380536660.6246160955150.09394865134180.183146954558-0.4538730163660.0263470863501-0.01398346434740.05856188794880.1871850392360.0191267336323-0.01364806302010.142864258678-0.04225856363480.39159860574416.49953545592.589586278054.83149010085
72.475860346-0.4779999257720.7963903118665.339995871791.475422143554.02612544064-0.202433348925-0.409047192839-0.06344574390850.4184241334570.228129227318-0.05897079877360.001891382049680.03006075614350.004265836217080.1838540624280.02659952654030.03506940050380.1982960124390.01315601501690.18414213165114.6991461474-2.84270516369.80255898852
82.49349233768-0.777214114581.148557349593.48494641794-0.194674356956.25895510674-0.036240383318-0.187517973925-0.09956773046140.2170839377410.2586867206190.3030067173910.0153076840193-0.530527347291-0.1765009028950.239292197038-0.05239719271120.08083844563250.214725629020.03092671130810.3084616665569.86006744545-6.377410999796.63220544832
90.9583020782670.2874141719040.5777984537614.640451342475.734135256097.288316097120.477224435216-0.513440682929-0.92730158895-0.182481659746-1.128143160441.041653678160.561224947152-1.455785552260.6195882877560.8286209918710.0720175517006-0.2072355718450.833394436646-0.1304462327260.95414126463430.706254045-21.537285067931.8992527419
102.158066757650.2789353842050.132729103432.727371785570.2176675776153.43918269040.09860088619050.4688829821840.0239932850756-0.0227714748457-0.113584244851-0.221235557663-0.2361818439210.2642555681910.08283787922360.2238534301360.0180103885035-0.005481325754660.4160518950710.006887120410250.23129522092532.444141485513.827721177942.5965361731
111.76185128344-0.277745398609-0.1346888079036.51737113511-1.903012542995.499202613210.1017652268020.6923087991350.126736977010.301637077952-0.324280436553-0.802343538927-0.2770357978510.751280685109-0.09532493947780.1767543182850.0189030142457-0.02314913408440.474116003728-0.01319685816340.3436598711440.98795453917.4829492543147.4397231139
121.42621296062-0.1617226580450.2111269789252.10540347674-0.3132510230352.733598523820.2198245200640.94411385533-0.208917370055-0.494609572583-0.3062375840250.1122039361120.00494498673856-0.0979402240089-0.0595501877730.3408541874440.0904854441326-0.06689657414420.567654598918-0.06882695846990.27481624745825.478900483910.310906627735.062108775
134.616712362810.3834041937960.5465678306234.69564109298-0.2324897921494.206034886630.1245711721180.371232578371-0.38553003918-0.177402970144-0.1508322023060.6987575286610.00904904713649-0.320832381599-0.107978612920.2119712689490.0406406771544-0.02026403555060.522232440763-0.08466486332030.38878235152116.537624881710.41606960542.8235074472
149.55335381252-0.47261988816-5.835400859160.06657267124960.7788807051968.991087232030.446816161608-0.523435676061.836877951420.521494814682-0.0382801611141.45496379466-0.609344865978-1.43403495847-0.2357553271480.278081636585-0.005819213722150.06732361525040.554788971523-0.04390166084870.7939985719642.000563236692.104794452671.03236051652
151.93169383327-1.94657650589-1.786884755764.002527356464.320091205744.85692272035-0.70781011668-0.857747703221-0.6708940727180.6369508335370.7362178009090.6160164133661.7121309402-0.117027396452-0.3411067552730.5384664904060.0484308259684-0.04767959458840.5375237088560.05269853795690.62075129225422.20876935310.20068802702547.8044379981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 142 )
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 237 )
9X-RAY DIFFRACTION9chain 'B' and (resid -6 through 7 )
10X-RAY DIFFRACTION10chain 'B' and (resid 8 through 80 )
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 95 )
12X-RAY DIFFRACTION12chain 'B' and (resid 96 through 197 )
13X-RAY DIFFRACTION13chain 'B' and (resid 198 through 236 )
14X-RAY DIFFRACTION14chain 'C' and (resid 307 through 311 )
15X-RAY DIFFRACTION15chain 'D' and (resid 305 through 311 )

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