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- PDB-8asc: Ku70/80 binds to the Ku-binding motif of PAXX -

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Basic information

Entry
Database: PDB / ID: 8asc
TitleKu70/80 binds to the Ku-binding motif of PAXX
Components
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
  • DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
  • Protein PAXX
KeywordsDNA BINDING PROTEIN / NHEJ / DNA repair
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / cellular hyperosmotic salinity response / 2-LTR circle formation / hematopoietic stem cell proliferation / telomeric DNA binding / positive regulation of protein kinase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / DNA polymerase binding / neurogenesis / activation of innate immune response / DNA helicase activity / telomere maintenance / cyclin binding / cellular response to leukemia inhibitory factor / small-subunit processome / Nonhomologous End-Joining (NHEJ) / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / 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 / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / ficolin-1-rich granule lumen / molecular adaptor activity / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 ...Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / Ku70, bridge and pillars domain superfamily / : / Ku70 / 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 / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor, type A domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / Protein PAXX
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSeif El Dahan, M. / Ropars, V. / Charbonnier, J.B.
Funding support France, 1items
OrganizationGrant numberCountry
French Alternative Energies and Atomic Energy Commission (CEA)ANR Break Dance France
CitationJournal: Sci Adv / Year: 2023
Title: PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
Authors: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / ...Authors: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / Madeleine Bossaert / Arun Prasad Pandurangan / Katheryn Meek / Tom L Blundell / Virginie Ropars / Patrick Calsou / Jean-Baptiste Charbonnier / Amanda K Chaplin /
Abstract: Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX ...Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX [paralog of x-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor (XLF)] in this mechanism. Here, we report high-resolution cryo-electron microscopy (cryo-EM) and x-ray crystallography structures of the PAXX C-terminal Ku-binding motif bound to Ku70/80 and cryo-EM structures of PAXX bound to two alternate DNA-dependent protein kinase (DNA-PK) end-bridging dimers, mediated by either Ku80 or XLF. We identify residues critical for the Ku70/PAXX interaction in vitro and in cells. We demonstrate that PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK dimers. Last, we show that engagement of both proteins provides a complementary advantage for DNA end synapsis and end joining in cells.
History
DepositionAug 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 6
B: X-ray repair cross-complementing protein 5
C: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
D: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
E: X-ray repair cross-complementing protein 6
F: X-ray repair cross-complementing protein 5
G: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
H: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
J: Protein PAXX
K: X-ray repair cross-complementing protein 6
L: X-ray repair cross-complementing protein 5
M: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
N: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
O: X-ray repair cross-complementing protein 6
P: X-ray repair cross-complementing protein 5
Q: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
R: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
T: Protein PAXX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)573,91122
Polymers573,52618
Non-polymers3844
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.024, 428.570, 96.065
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 33 through 223 or resid 233 through 534))
21(chain E and (resid 33 through 223 or resid 233 through 534))
31(chain K and (resid 33 through 223 or resid 233 through 534))
41(chain O and (resid 33 through 223 or resid 233 through 534))
12(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))
22(chain F and (resid 6 through 169 or resid 173...
32(chain L and (resid 6 through 169 or resid 180 through 543))
42(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))
13chain C
23(chain G and resid 0 through 18)
33chain M
43(chain Q and resid 0 through 18)
14chain D
24(chain H and resid 16 through 29)
34chain N
44(chain R and resid 16 through 29)
15chain J
25chain T

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERILEILE(chain A and (resid 33 through 223 or resid 233 through 534))AA33 - 22333 - 223
121PHEPHETYRTYR(chain A and (resid 33 through 223 or resid 233 through 534))AA233 - 534233 - 534
211SERSERILEILE(chain E and (resid 33 through 223 or resid 233 through 534))EE33 - 22333 - 223
221PHEPHETYRTYR(chain E and (resid 33 through 223 or resid 233 through 534))EE233 - 534233 - 534
311SERSERILEILE(chain K and (resid 33 through 223 or resid 233 through 534))KJ33 - 22333 - 223
321PHEPHETYRTYR(chain K and (resid 33 through 223 or resid 233 through 534))KJ233 - 534233 - 534
411SERSERILEILE(chain O and (resid 33 through 223 or resid 233 through 534))ON33 - 22333 - 223
421PHEPHETYRTYR(chain O and (resid 33 through 223 or resid 233 through 534))ON233 - 534233 - 534
112ASNASNLEULEU(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))BB6 - 16923 - 186
122ASPASPGLYGLY(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))BB173 - 174190 - 191
132PROPROLYSLYS(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))BB182 - 543199 - 560
212ASNASNLEULEU(chain F and (resid 6 through 169 or resid 173...FF6 - 16923 - 186
222ASPASPGLYGLY(chain F and (resid 6 through 169 or resid 173...FF173 - 174190 - 191
232PROPROLYSLYS(chain F and (resid 6 through 169 or resid 173...FF182 - 466199 - 483
242LYSLYSLYSLYS(chain F and (resid 6 through 169 or resid 173...FF469 - 543486 - 560
312ASNASNLEULEU(chain L and (resid 6 through 169 or resid 180 through 543))LK6 - 16923 - 186
322ASPASPLYSLYS(chain L and (resid 6 through 169 or resid 180 through 543))LK180 - 543197 - 560
412ASNASNLEULEU(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))PO6 - 16923 - 186
422ASPASPLYSLYS(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))PO180 - 466197 - 483
432LYSLYSLYSLYS(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))PO469 - 543486 - 560
113DCDCDTDTchain CCC0 - 181 - 19
213DCDCDTDT(chain G and resid 0 through 18)GG0 - 181 - 19
313DCDCDTDTchain MML0 - 181 - 19
413DCDCDTDT(chain Q and resid 0 through 18)QP0 - 181 - 19
114DGDGDGDGchain DDD16 - 292 - 15
214DGDGDGDG(chain H and resid 16 through 29)HH16 - 292 - 15
314DGDGDGDGchain NNM16 - 292 - 15
414DGDGDGDG(chain R and resid 16 through 29)RQ16 - 292 - 15
115ARGARGTHRTHRchain JJI177 - 2041 - 28
215ARGARGTHRTHRchain TTR177 - 2041 - 28

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(0.0288791695735, -0.0068562391336, -0.999559395709), (-0.202863536474, -0.979206645021, 0.000855521395743), (-0.97878106803, 0.202749447182, -0.0296695556666)56.677011888, -107.642787276, 71.06102645
2given(-0.99999750509, -0.00123564310169, 0.00186091375217), (0.00122911159569, -0.99999309544, -0.00350690135369), (0.00186523418184, -0.00350460533362, 0.99999211929)42.3572816682, -216.110114103, 47.6357517707
3given(-0.0270274566348, 0.00673742444461, 0.999611986573), (0.200830965542, 0.979625208005, -0.001172655617), (-0.979253000949, 0.200721346532, -0.0278298612841)-14.1771317148, -108.44650006, 118.83945631
4given(0.0916578636257, -0.119131041712, -0.988638776771), (-0.163140331448, -0.981200087795, 0.103109747191), (-0.982336026159, 0.151836038579, -0.109369781467)47.3389229362, -111.632204397, 69.4031911546
5given(-0.999999571199, -0.000914838684214, -0.000143776824327), (0.000914898373918, -0.999999495102, -0.00041563926798), (-0.000143396508853, -0.000415770630936, 0.999999903286)42.5908198637, -216.154028163, 48.0922187027
6given(-0.093173558402, 0.113060096009, 0.98920983755), (0.16201038144, 0.982012199051, -0.0969777150696), (-0.982380437672, 0.151226504306, -0.10981448026)-5.24162956212, -104.531238547, 117.404405388
7given(-0.79789895127, 0.27435536446, -0.536736804732), (-0.00199986119563, -0.891619005366, -0.452782011376), (-0.602787909731, -0.360200892923, 0.711970541961)67.9922474948, -80.7889703579, 3.89831162687
8given(-0.998154011977, 0.00758007702557, -0.0602586990137), (-0.00899575302725, -0.999689049544, 0.0232568409321), (-0.0600636728981, 0.0237559814563, 0.997911824032)44.7584422336, -216.830787339, 50.2084088981
9given(0.788370929199, -0.279354601665, 0.548117035425), (0.00784473820566, 0.895449658602, 0.445093663167), (-0.615150175223, -0.346599070162, 0.70813794312)-26.2977935628, -134.825291793, 53.0388206897
10given(-0.400520005668, 0.155761543492, -0.902951862852), (-0.0635807334128, -0.987794579537, -0.142194792366), (-0.914079436044, 0.000458482632003, 0.405534923768)68.7640660142, -100.854646525, 42.4720578107
11given(-0.999535758611, -0.0289124488095, -0.00960924351004), (0.0290640562536, -0.999448992184, -0.0160309905146), (-0.00914045354914, -0.0163028318593, 0.999825319635)40.2942543608, -215.676724326, 46.8182204795
12given(0.366994924216, -0.134579877077, 0.920436299961), (0.0747451056707, 0.990546107138, 0.115028599971), (-0.927215128639, 0.0265831961748, 0.373584580655)-25.0443842097, -114.218078386, 93.5620415636
13given(-0.998261435298, -0.0397030283321, 0.0435634748066), (0.0412858376978, -0.998496595148, 0.0360559160632), (0.0420664522102, 0.0377917850706, 0.998399816997)40.7715854003, -219.086135572, 46.9252300838

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Components

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X-ray repair cross-complementing protein ... , 2 types, 8 molecules AEKOBFLP

#1: Protein
X-ray repair cross-complementing protein 6 / 5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP- ...5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 1 / ATP-dependent DNA helicase II 70 kDa subunit / CTC box-binding factor 75 kDa subunit / CTCBF / DNA repair protein XRCC6 / Lupus Ku autoantigen protein p70 / Ku70 / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 6


Mass: 62629.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A C-terminal truncated version of Ku70 / Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Plasmid: pFL / Cell (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P12956, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Protein
X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase ...86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


Mass: 65356.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A C-terminal truncated version of Ku80 with a 10 histidines tag in N-terminal and a TEV-cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Plasmid: pFL / Cell (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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DNA chain , 2 types, 8 molecules CGMQDHNR

#3: DNA chain
DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')


Mass: 9313.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: DNA chain
DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')


Mass: 4546.936 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Protein/peptide , 1 types, 2 molecules JT

#5: Protein/peptide Protein PAXX / Paralog of XRCC4 and XLF / XRCC4-like small protein


Mass: 3068.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BUH6

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Non-polymers , 2 types, 24 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG- 3350; 0.1 M Bis-Tris Propane pH 8.5; 0.3 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.95→47.734 Å / Num. obs: 34200 / % possible obs: 86.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 67.64 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.098 / Rrim(I) all: 0.273 / Net I/σ(I): 6
Reflection shellResolution: 2.973→3.588 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1710 / CC1/2: 0.402 / Rpim(I) all: 0.695 / Rrim(I) all: 1.806 / % possible all: 53.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JEY

1jey


Resolution: 2.95→45.32 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2981 1995 5.84 %
Rwork0.252 32169 -
obs0.2547 34164 23.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 287.95 Å2 / Biso mean: 101.0598 Å2 / Biso min: 0.04 Å2
Refinement stepCycle: final / Resolution: 2.95→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33555 2788 20 20 36383
Biso mean--87.76 35.52 -
Num. residues----4317
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10120X-RAY DIFFRACTION10.711TORSIONAL
12E10120X-RAY DIFFRACTION10.711TORSIONAL
13K10120X-RAY DIFFRACTION10.711TORSIONAL
14O10120X-RAY DIFFRACTION10.711TORSIONAL
21B10583X-RAY DIFFRACTION10.711TORSIONAL
22F10583X-RAY DIFFRACTION10.711TORSIONAL
23L10583X-RAY DIFFRACTION10.711TORSIONAL
24P10583X-RAY DIFFRACTION10.711TORSIONAL
31C748X-RAY DIFFRACTION10.711TORSIONAL
32G748X-RAY DIFFRACTION10.711TORSIONAL
33M748X-RAY DIFFRACTION10.711TORSIONAL
34Q748X-RAY DIFFRACTION10.711TORSIONAL
41D548X-RAY DIFFRACTION10.711TORSIONAL
42H548X-RAY DIFFRACTION10.711TORSIONAL
43N548X-RAY DIFFRACTION10.711TORSIONAL
44R548X-RAY DIFFRACTION10.711TORSIONAL
51J272X-RAY DIFFRACTION10.711TORSIONAL
52T272X-RAY DIFFRACTION10.711TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.030.848310.34641920
3.03-3.110.498650.405762671
3.11-3.20.454570.37661391461
3.2-3.30.373170.3582362533
3.31-3.420.3379210.36993463674
3.42-3.560.4087440.35056416857
3.56-3.720.3718510.31338999509
3.72-3.920.304760.30431231130713
3.92-4.160.33751010.27711685178617
4.16-4.480.30861490.25942302245124
4.48-4.940.30061910.24223100329132
4.94-5.650.31552680.25834289455745
5.65-7.110.3574760.28567628810479
7.11-45.320.25155880.223495921018099
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)
10.1410.0999-0.04050.2632-0.15830.1289-0.0101-0.07-0.27270.2809-0.0433-0.40690.0952-0.0181-0.11450.2203-0.0942-0.08940.09020.29080.23468.6729-103.344319.9075
20.07050.0030.06940.13410.06780.2878-0.03040.1054-0.23330.1229-0.0643-0.19670.3101-0.30190.060.1282-0.0923-0.69980.10520.060.2156-0.37-70.36259.5571
3-0.00940.01030.0041-0.00030.0046-0.00640.0250.05030.10560.0240.0123-0.0575-0.01230.024400.8691-0.2712-0.17840.8789-0.1750.91365.8956-72.217333.6837
40.0011-0.00190.00660.0022-0.00450.00090.00290.02230.02060.04590.0477-0.0177-0.0328-0.085201.5278-0.0103-0.19861.3772-0.01131.46860.066-81.510229.7696
50.0986-0.1808-0.0230.0969-0.01290.24180.3728-0.1371-0.17680.0648-0.02730.1762-0.2912-0.28920.34450.15230.0838-0.57690.1950.1481-0.136437.6679-8.013840.7439
60.14760.02550.12630.0476-0.07840.1086-0.1458-0.22430.12870.37160.1898-0.1966-0.02310.14090.01910.0522-0.2108-0.61970.13520.01340.170946.454-41.364457.9906
70.00350.01040.0115-0.0005-0.00180.001-0.09330.04340.00590.08410.03390.02-0.0579-0.0219-00.9882-0.1711-0.15930.787-0.15830.943324.701-32.79749.9443
80.00290.0028-0.00920.00040.00260.00330.097-0.08570.0295-0.04940.10560.02730.0662-0.000101.1606-0.04310.18190.964-0.04911.192828.7513-25.751154.1458
90.0067-0.01050.00210.00360.00020.00110.009-0.07120.02760.01070.02850.01440.00620.02100.65780.03390.0450.78720.00510.644546.3439-6.620834.1242
100.1415-0.0053-0.05630.1280.14490.22790.1952-0.09450.28250.2791-0.31530.3835-0.01930.0547-0.09540.4592-0.03460.15030.087-0.15160.566233.7997-112.535467.7947
11-0.02560.0039-0.04970.1086-0.05290.14740.08950.09050.01410.3301-0.00550.3798-0.33710.16510.08170.12560.01390.69140.215-0.11740.052943.019-145.547257.6839
12-0.00530.0087-0.0015-0.0001-0.0034-0.00780.0339-0.0198-0.0478-0.00350.01830.0221-0.0732-0.0736-00.9668-0.15470.12810.92580.13981.119336.3813-143.647781.7583
13-0.00090.0030.0015-0.00270.001-0.0001-0.00360.0273-0.05260.03380.0610.02490.01250.065801.3624-0.13210.09751.21710.18111.232942.2827-134.383677.9155
140.0532-0.1460.13650.1158-0.04010.27120.3087-0.09880.05570.0801-0.02170.06530.31580.34440.21070.279-0.12330.23620.27680.00780.00014.8045-207.899288.7295
150.10660.0096-0.04130.03470.06460.17840.00080.0876-0.13170.29460.130.09850.1505-0.0412-0.01860.1504-0.05830.66860.277-0.11180.0534-3.6986-174.5643105.9453
160.00310.0037-0.02-0.0026-0.0015-0.001-0.0570.0912-0.00970.06890.0669-0.03680.03910.0798-01.041-0.27030.04460.68510.23661.011317.709-183.036697.8577
170.0046-0.00460.00580.0038-0.00170.00450.0325-0.0385-0.0436-0.01080.042-0.0117-0.0044-0.02501.254-0.0687-0.02951.0502-0.0441.306313.7949-190.081102.0324
18-0.0045-0.00060.0009-0.0001-0.0009-0-0.0206-0.0769-0.02390.007-0.00110.01010.0064-0.0073-00.82690.014-0.14330.9209-0.07310.7357-3.7667-208.899982.5596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 33 through 534)A33 - 534
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 544)B6 - 544
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 18)C0 - 18
4X-RAY DIFFRACTION4(chain 'D' and resid 16 through 29)D16 - 29
5X-RAY DIFFRACTION5(chain 'E' and resid 33 through 535)E33 - 535
6X-RAY DIFFRACTION6(chain 'F' and resid 4 through 543)F4 - 543
7X-RAY DIFFRACTION7(chain 'G' and resid 0 through 19)G0 - 19
8X-RAY DIFFRACTION8(chain 'H' and resid 15 through 29)H15 - 29
9X-RAY DIFFRACTION9(chain 'J' and resid 177 through 204)J177 - 204
10X-RAY DIFFRACTION10(chain 'K' and resid 33 through 535)K33 - 535
11X-RAY DIFFRACTION11(chain 'L' and resid 5 through 543)L5 - 543
12X-RAY DIFFRACTION12(chain 'M' and resid 0 through 18)M0 - 18
13X-RAY DIFFRACTION13(chain 'N' and resid 16 through 29)N16 - 29
14X-RAY DIFFRACTION14(chain 'O' and resid 33 through 535)O33 - 535
15X-RAY DIFFRACTION15(chain 'P' and resid 4 through 543)P4 - 543
16X-RAY DIFFRACTION16(chain 'Q' and resid 0 through 19)Q0 - 19
17X-RAY DIFFRACTION17(chain 'R' and resid 15 through 29)R15 - 29
18X-RAY DIFFRACTION18(chain 'T' and resid 177 through 204)T177 - 204

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