PDB-5jx8: New improved structure of D4 in trigonal space group

ID or keywords:

Entry

Database: PDB / ID: 5jx8

Title

New improved structure of D4 in trigonal space group

Components

Uracil-DNA glycosylase

Keywords

HYDROLASE /

DNA Repair Enzyme Component of Processivity Factor Poxvirus

Function / homology

Function and homology information

uracil-DNA glycosylase / uracil DNA N-glycosylase activity /

DNA repair /

Biological species

Vaccinia virus

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Schormann, N. / Chattopadhyay, D.

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2016
Title: Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases.
Authors: Schormann, N. / Zhukovskaya, N. / Bedwell, G. / Nuth, M. / Gillilan, R. / Prevelige, P.E. / Ricciardi, R.P. / Banerjee, S. / Chattopadhyay, D.

History

Deposition	May 12, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5jx8.cif.gz	198.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5jx8.ent.gz	158.7 KB	Display	PDB format
PDBx/mmJSON format	5jx8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jx/5jx8 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/5jx8	HTTPS FTP

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Related structure data

Related structure data	5jx0C 5jx3C 2owqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1op8-3 5dtu-d 5i0m-d 1r74-d 2noa-d 6vi1-1 2ofk-d 3nmn-2 4l5b-d 3eis-5 Search similar-shape structures by Omokage search (details) 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: Uracil-DNA glycosylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	85.130, 85.130, 139.050
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Uracil-DNA glycosylase / / UDG Mass: 27253.119 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus (strain Western Reserve) Strain: Western Reserve / Gene: UNG, TS17, VACWR109, D4R / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P04303, uracil-DNA glycosylase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	Western Reserve (WR109) vaccinia virus strain was used. The closest sequence database entry is: ...Western Reserve (WR109) vaccinia virus strain was used. The closest sequence database entry is: AA089388. Any sequence difference from this entry except for the engineered mutations in the D4 mutants is unintentional

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.74 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: 1.5M (NH4)2SO4, 12% Glycerol, 0.1M Hepes

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 25, 2011 / Details: Mirrors
Radiation	Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→42.57 Å / Num. obs: 39960 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / B_iso Wilson estimate: 39.1 Å² / CC_1/2: 1 / R_merge(I) obs: 0.034 / Net I/σ(I): 26.7
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.614 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2142: ???)	refinement
XDS	March 30, 2013	data reduction
Aimless	0.5.17	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OWQ

2owq

Resolution: 2→19.62 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.93

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2497	1998	5.01 %	Random selection
R_work	0.2016	-	-	-
obs	0.204	39845	99.53 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 50.4 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3615	0	39	150	3804

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3748
X-RAY DIFFRACTION	f_angle_d	0.92	5092
X-RAY DIFFRACTION	f_dihedral_angle_d	13.14	2218
X-RAY DIFFRACTION	f_chiral_restr	0.052	555
X-RAY DIFFRACTION	f_plane_restr	0.006	638

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 (%)
2.0001-2.05	0.3537	122	0.3091	2703	X-RAY DIFFRACTION	100
2.05-2.1054	0.3352	159	0.2963	2650	X-RAY DIFFRACTION	100
2.1054-2.1673	0.3401	142	0.2759	2670	X-RAY DIFFRACTION	100
2.1673-2.2371	0.3024	139	0.2498	2699	X-RAY DIFFRACTION	100
2.2371-2.317	0.3252	139	0.2281	2673	X-RAY DIFFRACTION	100
2.317-2.4096	0.2642	138	0.2212	2700	X-RAY DIFFRACTION	100
2.4096-2.519	0.2971	142	0.2334	2692	X-RAY DIFFRACTION	100
2.519-2.6515	0.2516	142	0.228	2699	X-RAY DIFFRACTION	100
2.6515-2.8172	0.2989	138	0.2369	2721	X-RAY DIFFRACTION	100
2.8172-3.034	0.2912	154	0.2347	2674	X-RAY DIFFRACTION	100
3.034-3.338	0.2718	170	0.2163	2703	X-RAY DIFFRACTION	100
3.338-3.8179	0.2388	141	0.1819	2718	X-RAY DIFFRACTION	99
3.8179-4.7985	0.1954	144	0.1596	2759	X-RAY DIFFRACTION	99
4.7985-19.6207	0.1972	128	0.1688	2786	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.0331	0.0197	0.0354	0.0191	0.0098	0.0299	-0.0292	0.0189	-0.0529	-0.1218	-0.026	-0.2651	0.0186	0.0751	0.0001	0.3903	0.111	-0.009	0.4935	0.1105	0.4449	-19.2767	13.7844	-4.2144
2	0.0248	0.0036	-0.0153	0.0652	-0.0263	0.0259	0.0485	0.0169	-0.1443	-0.1073	0.0605	0.0808	0.0456	-0.2355	0.0035	0.2397	0.0486	-0.0524	0.4615	0.1085	0.3592	-24.7804	12.008	7.4462
3	0.0283	0.0001	0.0365	0.0152	-0.0157	0.0365	0.1418	-0.1884	0.0786	-0.1418	-0.0069	0.0091	-0.02	0.0159	-0.0001	0.2666	0.0189	0.0496	0.4689	0.0739	0.351	-13.5897	16.4752	10.3971
4	0.1221	0.065	0.124	0.0768	0.0733	0.1266	0.0086	-0.1083	0.2088	-0.1975	-0.0819	-0.0533	-0.3413	0.1898	-0.0299	0.2573	-0.0686	0.0518	0.5903	0.0632	0.3937	-3.7615	19.7776	14.511
5	0.0076	0.0069	-0.0035	0.0154	-0.0189	0.0251	0.1008	-0.1735	-0.0368	0.0824	-0.0221	0.0802	0.0094	-0.1086	0.0092	0.22	0.0223	0.0023	0.5794	0.1449	0.351	-19.7222	8.3264	15.4148
6	0.0059	-0.0127	0.0053	0.0198	-0.0108	0.0042	0.0379	-0.1126	-0.0186	0.0666	-0.0081	0.1206	0.0815	0.0139	-0.0002	0.2344	-0.0456	0.0464	0.58	0.0884	0.346	-10.5901	8.562	23.3167
7	0.0443	-0.0586	0.0243	0.0593	-0.0312	0.0204	0.0588	-0.1157	0.1139	-0.0274	0.0834	0.0199	0.017	-0	-0.0047	0.2967	-0.1095	0.0007	0.7702	0.1197	0.4843	-5.8345	8.4071	24.4765
8	0.0451	0.0364	-0.0589	0.031	-0.0491	0.0813	0.055	-0.2078	0.1079	0.0762	-0.0403	0.0103	-0.0353	0.0913	0.0219	0.1896	0.0326	-0.0144	0.851	0.0989	0.404	5.0588	5.7255	20.9629
9	0.0939	0.0308	0.0196	0.0868	0.0097	0.0278	0.1093	0.069	-0.0311	-0.0284	0.0709	-0.0467	-0.068	0.073	0.102	0.1077	-0.0477	0.1711	0.7945	0.1474	0.4157	4.6899	8.3536	9.049
10	0.1055	-0.0387	-0.0705	0.0529	0.0067	0.1551	0.1837	-0.0478	-0.12	-0.0621	-0.0394	0.1958	-0.3546	-0.3363	0.1623	0.4941	0.5008	-0.0128	0.3843	0.1031	0.3867	-37.5205	28.8333	-10.4134
11	0.0789	0.0359	-0.133	0.0805	-0.08	0.2527	0.2255	0.1892	-0.2112	-0.3748	0.0391	0.2145	-0.1549	-0.5329	0.1186	0.4967	0.5061	-0.1149	0.228	0.1505	0.3463	-31.3915	21.672	-17.4966
12	0.0707	-0.0544	0.045	0.1078	-0.0582	0.0322	0.0522	0.1511	0.0582	-0.1142	-0.0384	0.0005	-0	-0.0663	-0.0063	0.6383	0.3108	0.0201	0.3576	0.1206	0.3528	-25.8239	27.88	-24.5304
13	0.0412	-0.0255	0.013	0.0176	-0.0167	0.0184	0.1358	0.0861	0.0096	-0.1607	-0.03	0.0478	0.0131	0.0347	0	0.879	0.2904	0.0022	0.4572	0.0653	0.4985	-23.3576	23.4734	-25.7054
14	0.0316	-0.0045	0.0413	0.0722	0.0157	0.1054	0.1787	0.0757	-0.1017	-0.2678	0.0432	-0.2463	0.0185	0.0288	0.0131	0.4361	0.1615	0.0599	0.2629	0.0339	0.3837	-17.7179	14.5846	-17.0436

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -8 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 71 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 133 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 134 through 151 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 152 through 168 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 169 through 187 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 188 through 204 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 205 through 218 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid -2 through 86 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 87 through 151 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 152 through 168 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 169 through 187 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 188 through 218 )

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