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- PDB-9wvi: Crystal structure of TONSL UBL mutant - R934W -

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Basic information

Entry
Database: PDB / ID: 9wvi
TitleCrystal structure of TONSL UBL mutant - R934W
ComponentsTonsoku-like protein
KeywordsCHAPERONE / TONSL / Sponastrime dysplasia / Mutation / Oligomerisation / DNA repair
Function / homology
Function and homology information


histone reader activity / nuclear replication fork / replication fork processing / protein localization to chromatin / double-strand break repair via homologous recombination / site of double-strand break / histone binding / nuclear body / nucleoplasm / cytoplasm
Similarity search - Function
: / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...: / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Leucine-rich repeat domain superfamily / Ankyrin repeat-containing domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Tonsoku-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKarmakar, A. / Roy, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2022/001895 India
CitationJournal: To Be Published
Title: Crystal structure of TONSL UBL mutant - R934W
Authors: Karmakar, A. / Roy, S.
History
DepositionSep 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tonsoku-like protein
B: Tonsoku-like protein
C: Tonsoku-like protein
D: Tonsoku-like protein


Theoretical massNumber of molelcules
Total (without water)39,2004
Polymers39,2004
Non-polymers00
Water1,928107
1
A: Tonsoku-like protein


Theoretical massNumber of molelcules
Total (without water)9,8001
Polymers9,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tonsoku-like protein


Theoretical massNumber of molelcules
Total (without water)9,8001
Polymers9,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tonsoku-like protein


Theoretical massNumber of molelcules
Total (without water)9,8001
Polymers9,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tonsoku-like protein


Theoretical massNumber of molelcules
Total (without water)9,8001
Polymers9,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.884, 81.109, 102.497
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 932 through 949 or resid 953 through 1010))
d_2ens_1(chain "B" and (resid 932 through 949 or resid 953 through 1010))
d_3ens_1(chain "C" and (resid 932 through 1009 or (resid 1010...
d_4ens_1(chain "D" and (resid 932 through 949 or resid 953 through 1010))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISPROPROAA932 - 9496 - 23
d_12ASPASPTRPTRPAA953 - 101027 - 84
d_21HISHISPROPROBB932 - 9496 - 23
d_22ASPASPTRPTRPBB953 - 101027 - 84
d_31HISHISTRPTRPCC932 - 10106 - 84
d_41HISHISPROPRODD932 - 9496 - 23
d_42ASPASPTRPTRPDD953 - 101027 - 84

NCS oper:
IDCodeMatrixVector
1given(0.964234732042, -0.0338345801084, -0.262881347213), (-0.13240101235, 0.797721202666, -0.588311868608), (0.229611309505, 0.602076493483, 0.764710757439)-18.2001997952, -25.1121448768, 9.07675235167
2given(-0.979663915686, 0.0577137724112, -0.192165899102), (0.0615112598532, -0.825234704526, -0.561430358422), (-0.190984232896, -0.561833429871, 0.804902615143)7.64932472493, -13.4302921122, 25.3366344478
3given(-0.88325053727, 0.260937351607, -0.389589767511), (0.295494629246, -0.335367640058, -0.894545398562), (-0.364076108114, -0.905229387801, 0.219108062295)0.654070762399, -9.30284111316, -6.37022395942

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Components

#1: Protein
Tonsoku-like protein / Inhibitor of kappa B-related protein / I-kappa-B-related protein / IkappaBR / NF-kappa-B inhibitor- ...Inhibitor of kappa B-related protein / I-kappa-B-related protein / IkappaBR / NF-kappa-B inhibitor-like protein 2 / Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2


Mass: 9800.007 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TONSL, IKBR, NFKBIL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Escherichia coli / References: UniProt: Q96HA7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.15 M Calcium chloride dihydrate, 0.1 M MES 6.2, 15 % v/v PEG 3350, 5 % v/v Glycerol
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS DIAMOND MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 15, 2024 / Details: HELIOS EF
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.19→40.55 Å / Num. obs: 17783 / % possible obs: 99.91 % / Redundancy: 7.5 % / Biso Wilson estimate: 41.54 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.04671 / Rrim(I) all: 0.1286 / Net I/σ(I): 12.24
Reflection shellResolution: 2.19→2.33 Å / Redundancy: 7 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 5511 / CC1/2: 0.543 / CC star: 0.839 / Rpim(I) all: 0.5516 / Rrim(I) all: 1.463 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PROTEUM PLUSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→40.55 Å / SU ML: 0.2371 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2432 890 5 %
Rwork0.2045 16893 -
obs0.2065 17783 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.05 Å2
Refinement stepCycle: LAST / Resolution: 2.19→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 0 107 2657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762616
X-RAY DIFFRACTIONf_angle_d0.94713591
X-RAY DIFFRACTIONf_chiral_restr0.0617416
X-RAY DIFFRACTIONf_plane_restr0.009461
X-RAY DIFFRACTIONf_dihedral_angle_d19.2617933
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.21399021489
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.02347659647
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.899766983278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.330.32571450.26912758X-RAY DIFFRACTION99.9
2.33-2.510.30621460.24962767X-RAY DIFFRACTION100
2.51-2.760.28961450.25242762X-RAY DIFFRACTION99.97
2.76-3.160.27881480.21622802X-RAY DIFFRACTION99.93
3.16-3.980.23431490.18332835X-RAY DIFFRACTION99.97
3.98-40.550.20761570.18642969X-RAY DIFFRACTION99.74
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)
14.97917058679-0.5450939896570.07345373966674.16632670342-0.2526849282056.973823922460.0468105637345-0.0833551095817-0.0993634214339-0.303702195513-0.1449733069020.160498586234-0.0532547176447-0.07468195829340.04129191340270.2990920512160.0686236770704-0.007196260323340.2464158009290.02710878991890.2313520262110.468-2.49-21.623
24.656138461271.668942903251.014734136265.03020294146-3.391861002626.38029111034-0.126346479672-0.439993051422-0.266290918589-0.2232288750330.0020318979776-0.03374668710950.429849861294-0.3278041541660.03172701645030.3253038464070.02098094379870.0431199279350.3012506156020.06647965446330.380891333492-2.694-15.657-6.77
33.77122557919-0.391531170394-1.049693481075.77736246898-0.6607276277099.15153812905-0.06984731571-0.310051494877-0.0822401393950.258931691620.03687342538170.1918316477010.247831370874-0.1867975073730.06861972788210.3000318873390.0272372891013-0.01433844538560.358157393562-0.03657033729330.2079610613511.0571.6467.457
45.548429065990.8348908286740.4321824877558.46847431375-0.6498031596224.71365875855-0.107604530106-0.08185808443380.355203503051-0.2153424913760.0273644814799-0.0266069921599-0.6406484544870.075323644758-0.001950816728390.4693361546160.0852985600876-0.02782108819630.3068046156920.03883490573260.272415737962-0.68513.971-12.682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 932:1011 )A932 - 1011
2X-RAY DIFFRACTION2( CHAIN B AND RESID 931:1011 )B931 - 1011
3X-RAY DIFFRACTION3( CHAIN C AND RESID 932:1010 )C932 - 1010
4X-RAY DIFFRACTION4( CHAIN D AND RESID 932:1011 )D932 - 1011

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