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- PDB-9rqp: Human SMUG1 in complex with 5-fluorouracil -

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Basic information

Entry
Database: PDB / ID: 9rqp
TitleHuman SMUG1 in complex with 5-fluorouracil
ComponentsSingle-strand selective monofunctional uracil DNA glycosylase
KeywordsHYDROLASE / SMUG1 / 5-fluorouracil / 5-fU
Function / homology
Function and homology information


single-strand selective uracil DNA N-glycosylase activity / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / base-excision repair ...single-strand selective uracil DNA N-glycosylase activity / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / base-excision repair / fibrillar center / nucleolus / DNA binding / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Single-strand selective monofunctional uracil DNA glycosylase / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / R-1,2-PROPANEDIOL / 5-FLUOROURACIL / Single-strand selective monofunctional uracil DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsLudaescher, J.M. / Scaletti Hutchinson, E. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: To Be Published
Title: Human SMUG1 in complex with 5-fluorouracil
Authors: Ludaescher, J.M. / Scaletti Hutchinson, E. / Stenmark, P.
History
DepositionJun 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-strand selective monofunctional uracil DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9998
Polymers27,3741
Non-polymers6257
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint15 kcal/mol
Surface area10760 Å2
Unit cell
Length a, b, c (Å)48.558, 59.975, 91.293
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Single-strand selective monofunctional uracil DNA glycosylase


Mass: 27373.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMUG1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53HV7, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 5 types, 110 molecules

#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Buffer System 3 pH 8.4, 80 % (v/v) P500MME_P20K, 0.12 M Alcohols Mix (Morpheus Screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.899→50.126 Å / Num. obs: 21518 / % possible obs: 99.2 % / Redundancy: 12.4 % / CC1/2: 0.993 / Net I/σ(I): 7.5
Reflection shellResolution: 1.899→1.932 Å / Num. unique obs: 1090 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
AutoProcessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.899→50.126 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.545 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2333 1104 5.143 %
Rwork0.1905 20364 -
all0.193 --
obs-21468 98.899 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.196 Å2-0 Å2-0 Å2
2--0.74 Å2-0 Å2
3----0.544 Å2
Refinement stepCycle: LAST / Resolution: 1.899→50.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 37 103 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122022
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161963
X-RAY DIFFRACTIONr_angle_refined_deg1.631.8542742
X-RAY DIFFRACTIONr_angle_other_deg0.521.7274507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.03518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67310323
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0531092
X-RAY DIFFRACTIONr_chiral_restr0.0750.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
X-RAY DIFFRACTIONr_nbd_refined0.220.2417
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21812
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2980
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.282
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.211
X-RAY DIFFRACTIONr_nbd_other0.1660.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.211
X-RAY DIFFRACTIONr_mcbond_it2.0822.582988
X-RAY DIFFRACTIONr_mcbond_other2.0672.582988
X-RAY DIFFRACTIONr_mcangle_it2.9794.6241235
X-RAY DIFFRACTIONr_mcangle_other2.9784.6281236
X-RAY DIFFRACTIONr_scbond_it3.2493.0181034
X-RAY DIFFRACTIONr_scbond_other3.2483.021035
X-RAY DIFFRACTIONr_scangle_it5.0115.3381507
X-RAY DIFFRACTIONr_scangle_other5.015.341508
X-RAY DIFFRACTIONr_lrange_it6.43527.2222227
X-RAY DIFFRACTIONr_lrange_other6.4627.2062218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.9490.402790.3821465X-RAY DIFFRACTION97.168
1.949-2.0020.317740.2871455X-RAY DIFFRACTION99.7391
2.002-2.060.311710.2711414X-RAY DIFFRACTION99.9327
2.06-2.1230.283750.2731383X-RAY DIFFRACTION99.863
2.123-2.1930.207720.2121334X-RAY DIFFRACTION100
2.193-2.2690.3710.2461289X-RAY DIFFRACTION99.7799
2.269-2.3550.287670.1991250X-RAY DIFFRACTION100
2.355-2.4510.231600.1751198X-RAY DIFFRACTION100
2.451-2.5590.216670.1731180X-RAY DIFFRACTION100
2.559-2.6840.28520.1841096X-RAY DIFFRACTION98.9655
2.684-2.8290.273640.1811052X-RAY DIFFRACTION100
2.829-30.208640.1621006X-RAY DIFFRACTION100
3-3.2060.229540.16945X-RAY DIFFRACTION100
3.206-3.4620.221480.169841X-RAY DIFFRACTION94.8773
3.462-3.790.217500.157755X-RAY DIFFRACTION92.5287
3.79-4.2350.133350.139695X-RAY DIFFRACTION93.1122
4.235-4.8840.2360.148673X-RAY DIFFRACTION100
4.884-5.9680.196280.182589X-RAY DIFFRACTION100
5.968-8.380.212260.172452X-RAY DIFFRACTION100
8.38-50.1260.242110.19292X-RAY DIFFRACTION100

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