PDB-8ain: MCUGI SAUNG complex

ID or keywords:

Entry

Database: PDB / ID: 8ain

Title

MCUGI SAUNG complex

Components

MCUGI
Uracil-DNA glycosylase

Keywords

PROTEIN 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

Biological species

Staphylococcus aureus (bacteria)

Macrococcus caseolyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Muselmani, W. / Savva, R.

Funding support

United Kingdom, 1items

Citation

Journal: 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

Deposition	Jul 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 21, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2023	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ain.cif.gz	141.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8ain.ent.gz	107.5 KB	Display	PDB format
PDBx/mmJSON format	8ain.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ain_validation.pdf.gz	453.1 KB	Display	wwPDB validaton report
Full document	8ain_full_validation.pdf.gz	454 KB	Display
Data in XML	8ain_validation.xml.gz	13.3 KB	Display
Data in CIF	8ain_validation.cif.gz	17.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ai/8ain ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8ain	HTTPS FTP

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Related structure data

Related structure data	8ailC 8aimC 3wdgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uracil-DNA glycosylase

B: MCUGI

hetero molecules

40.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	91.522, 91.522, 158.620
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	182
Space group name H-M	P6₃22

#1: Protein	Uracil-DNA glycosylase / UDG Mass: 26071.443 Da / Num. of mol.: 1 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
#2: Protein	MCUGI Mass: 14146.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrococcus caseolyticus (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.41 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 1 M ammonium sulphate, 0.2 M sodium chloride, 9.55%(w/v) PEG 20.000, 0.1 M MES, at pH 6.5

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Data collection

Diffraction	Mean temperature: 289.15 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9198 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9198 Å / Relative weight: 1
Reflection	Resolution: 2.7→45.8 Å / Num. obs: 11391 / % possible obs: 100 % / Redundancy: 11.9 % / CC_1/2: 0.993 / Net I/σ(I): 2.12
Reflection shell	Resolution: 2.7→2.83 Å / Num. unique obs: 1470 / CC_1/2: 0.55

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WDG

3wdg

Resolution: 2.7→45.8 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.908 / SU B: 16.126 / SU ML: 0.315 / Cross valid method: FREE R-VALUE / ESU R: 1.2 / ESU R Free: 0.357
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2605	581	5.105 %
R_work	0.1981	10799	-
all	0.202	-	-
obs	-	11380	99.763 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 46.431 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.532 Å²	-0.766 Å²	-0 Å²
2-	-	-1.532 Å²	0 Å²
3-	-	-	4.969 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→45.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2645	0	9	17	2671

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	2731
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2523
X-RAY DIFFRACTION	r_angle_refined_deg	1.586	1.642	3703
X-RAY DIFFRACTION	r_angle_other_deg	1.21	1.578	5830
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.537	5	320
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.35	23.611	144
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.829	15	464
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.465	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	352
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3044
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	626
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	569
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	2406
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1278
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1304
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	62
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.139	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.227	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.105	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.827	4.714	1289
X-RAY DIFFRACTION	r_mcbond_other	3.78	4.713	1288
X-RAY DIFFRACTION	r_mcangle_it	5.858	7.055	1606
X-RAY DIFFRACTION	r_mcangle_other	5.861	7.058	1607
X-RAY DIFFRACTION	r_scbond_it	4.062	5.152	1441
X-RAY DIFFRACTION	r_scbond_other	4.049	5.145	1438
X-RAY DIFFRACTION	r_scangle_it	6.311	7.554	2097
X-RAY DIFFRACTION	r_scangle_other	6.309	7.543	2092
X-RAY DIFFRACTION	r_lrange_it	8.198	53.621	3003
X-RAY DIFFRACTION	r_lrange_other	8.197	53.646	3004

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7-2.77	0.358	40	0.268	796	X-RAY DIFFRACTION	100
2.77-2.846	0.342	35	0.28	740	X-RAY DIFFRACTION	99.8711
2.846-2.929	0.332	42	0.269	737	X-RAY DIFFRACTION	100
2.929-3.019	0.278	32	0.272	706	X-RAY DIFFRACTION	100
3.019-3.118	0.291	42	0.279	701	X-RAY DIFFRACTION	100
3.118-3.227	0.312	43	0.254	672	X-RAY DIFFRACTION	100
3.227-3.349	0.348	41	0.217	640	X-RAY DIFFRACTION	100
3.349-3.486	0.246	28	0.2	636	X-RAY DIFFRACTION	100
3.486-3.64	0.309	29	0.182	619	X-RAY DIFFRACTION	100
3.64-3.818	0.235	27	0.17	592	X-RAY DIFFRACTION	99.6779
3.818-4.024	0.243	25	0.165	558	X-RAY DIFFRACTION	99.8288
4.024-4.268	0.199	26	0.155	532	X-RAY DIFFRACTION	99.8211
4.268-4.563	0.212	27	0.133	500	X-RAY DIFFRACTION	99.8106
4.563-4.928	0.202	26	0.134	473	X-RAY DIFFRACTION	99.8
4.928-5.398	0.197	23	0.156	436	X-RAY DIFFRACTION	99.5662
5.398-6.034	0.411	20	0.228	395	X-RAY DIFFRACTION	99.7596
6.034-6.966	0.313	17	0.22	360	X-RAY DIFFRACTION	99.4723
6.966-8.527	0.172	26	0.171	302	X-RAY DIFFRACTION	99.3939
8.527-9.612	0.195	18	0.172	248	X-RAY DIFFRACTION	98.5185
9.612-10.722	0.382	14	0.307	156	X-RAY DIFFRACTION	94.9721

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