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- PDB-8aim: Ugi-2 SAUNG complex -

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Basic information

Entry
Database: PDB / ID: 8aim
TitleUgi-2 SAUNG complex
Components
  • Uracil-DNA glycosylase
  • Uracil-DNA glycosylase inhibitor
KeywordsPROTEIN BINDING / Ugi / Ung / complex / inhibitor
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm
Similarity search - Function
Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like ...Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesBacillus phage vB_BpuM-BpSp (virus)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMuselmani, W. / Savva, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Birkbeck College United Kingdom
CitationJournal: Viruses / Year: 2023
Title: A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase.
Authors: Muselmani, W. / Kashif-Khan, N. / Bagneris, C. / Santangelo, R. / Williams, M.A. / Savva, R.
History
DepositionJul 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Uracil-DNA glycosylase inhibitor
G: Uracil-DNA glycosylase inhibitor
A: Uracil-DNA glycosylase
E: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)72,9984
Polymers72,9984
Non-polymers00
Water88349
1
B: Uracil-DNA glycosylase inhibitor
A: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)36,4992
Polymers36,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-10 kcal/mol
Surface area13280 Å2
MethodPISA
2
G: Uracil-DNA glycosylase inhibitor
E: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)36,4992
Polymers36,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-11 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.652, 142.816, 82.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21G
32A
42E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSSERSERBA3 - 883 - 88
221LYSLYSSERSERGB3 - 883 - 88
332METMETCYSCYSAC1 - 2141 - 214
442METMETCYSCYSED1 - 2141 - 214

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Protein Uracil-DNA glycosylase inhibitor


Mass: 10427.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage vB_BpuM-BpSp (virus) / Gene: Bp8pS_259 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A141HSF0
#2: Protein Uracil-DNA glycosylase / UDG


Mass: 26071.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ung, A6762_02745, C7P97_05245, CSC87_03540, CV021_15850, E3A28_05745, E3K14_03025, GO782_00930, GO788_12235, NCTC6133_00684, NCTC7878_01215, NCTC7972_01353, QU38_09915, SAMEA70245418_01578
Production host: Escherichia coli (E. coli) / References: UniProt: A0A5F0HLK2, uracil-DNA glycosylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 70% v/v MPD

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Data collection

DiffractionMean temperature: 289.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→52.92 Å / Num. obs: 25462 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.98 / Net I/σ(I): 1.62
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 3052 / CC1/2: 0.528

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDG, 1UDI

3wdg

1udi


Resolution: 2.6→52.92 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.686 / SU ML: 0.268 / Cross valid method: FREE R-VALUE / ESU R: 0.564 / ESU R Free: 0.293
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2456 1215 4.772 %
Rwork0.202 24247 -
all0.204 --
obs-25462 99.922 %
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: 43.352 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2---1.779 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.6→52.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 0 49 4951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135032
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164652
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.6446822
X-RAY DIFFRACTIONr_angle_other_deg1.2121.58110800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2195599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26124.015264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09415883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0121518
X-RAY DIFFRACTIONr_chiral_restr0.0650.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021105
X-RAY DIFFRACTIONr_nbd_refined0.2140.2912
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24264
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22380
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2121
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.29
X-RAY DIFFRACTIONr_nbd_other0.20.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.24
X-RAY DIFFRACTIONr_mcbond_it3.0534.4542408
X-RAY DIFFRACTIONr_mcbond_other3.0244.4532407
X-RAY DIFFRACTIONr_mcangle_it4.7416.6713003
X-RAY DIFFRACTIONr_mcangle_other4.7416.6733004
X-RAY DIFFRACTIONr_scbond_it3.3884.7632624
X-RAY DIFFRACTIONr_scbond_other3.3884.7632624
X-RAY DIFFRACTIONr_scangle_it5.3016.9923819
X-RAY DIFFRACTIONr_scangle_other5.3016.9933820
X-RAY DIFFRACTIONr_lrange_it7.23149.5245361
X-RAY DIFFRACTIONr_lrange_other7.23349.5285357
X-RAY DIFFRACTIONr_ncsr_local_group_10.1420.052483
X-RAY DIFFRACTIONr_ncsr_local_group_20.0990.056989
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.141510.05008
12GX-RAY DIFFRACTIONLocal ncs0.141510.05008
23AX-RAY DIFFRACTIONLocal ncs0.098590.05008
24EX-RAY DIFFRACTIONLocal ncs0.098590.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.312830.281766X-RAY DIFFRACTION99.892
2.668-2.7410.3141040.3131696X-RAY DIFFRACTION99.8336
2.741-2.820.403950.2941672X-RAY DIFFRACTION99.8305
2.82-2.9070.356820.3061626X-RAY DIFFRACTION100
2.907-3.0020.34730.2851605X-RAY DIFFRACTION100
3.002-3.1070.27670.2461534X-RAY DIFFRACTION99.9376
3.107-3.2240.241690.2081494X-RAY DIFFRACTION100
3.224-3.3560.281770.2171395X-RAY DIFFRACTION100
3.356-3.5050.234720.1961373X-RAY DIFFRACTION100
3.505-3.6760.241640.1921327X-RAY DIFFRACTION100
3.676-3.8740.239830.1761214X-RAY DIFFRACTION99.923
3.874-4.1090.196600.1631196X-RAY DIFFRACTION99.9204
4.109-4.3920.194420.1631132X-RAY DIFFRACTION100
4.392-4.7430.155380.151066X-RAY DIFFRACTION99.9095
4.743-5.1950.173510.15968X-RAY DIFFRACTION100
5.195-5.8060.226420.176872X-RAY DIFFRACTION100
5.806-6.70.228380.184788X-RAY DIFFRACTION100
6.7-8.1970.285300.166672X-RAY DIFFRACTION100
8-100.227140.2322X-RAY DIFFRACTION98.5337
8.197-11.5520.23310.142529X-RAY DIFFRACTION99.6441

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