PDB-5y5o: Crystal structure of the dUTPase of white spot syndrome virus in ...

ID or keywords:

Entry

Database: PDB / ID: 5y5o

Title

Crystal structure of the dUTPase of white spot syndrome virus in the apo state

Components

Wsv112

Keywords

VIRAL PROTEIN / dUTPase / WSSV / pyrophosphatase / dUTP

Function / homology

Function and homology information

dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function

Biological species

White spot syndrome virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Ma, Q. / Zang, K.

Funding support

China, 2items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner.
Authors: Zang, K. / Li, F. / Ma, Q.

History

Deposition	Aug 9, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 6, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 31, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3	Nov 22, 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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Validation report

Summary document	5y5o_validation.pdf.gz	477.7 KB	Display	wwPDB validaton report
Full document	5y5o_full_validation.pdf.gz	481.4 KB	Display
Data in XML	5y5o_validation.xml.gz	32.1 KB	Display
Data in CIF	5y5o_validation.cif.gz	44.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y5/5y5o ftp://data.pdbj.org/pub/pdb/validation_reports/y5/5y5o	HTTPS FTP

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Related structure data

Related structure data	5y5pC 5y5qC 3c3iS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1jwb-1 5nau-d 4w6v-d 2p2f-2 7kw0-2 5jjq-1 7l4g-3 5l25-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (5)

Deposited unit

A: Wsv112

B: Wsv112

C: Wsv112

D: Wsv112

E: Wsv112

F: Wsv112

114 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Wsv112

B: Wsv112

C: Wsv112

defined by author&software
Evidence: gel filtration
57.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Wsv112

E: Wsv112

F: Wsv112

defined by author&software
57.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.230, 97.290, 107.470
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Wsv112 Mass: 19029.248 Da / Num. of mol.: 6 / Fragment: UNP residues 1-171 Source method: isolated from a genetically manipulated source Source: (gene. exp.) White spot syndrome virus (isolate Shrimp/China/Tongan/1996) Strain: isolate Shrimp/China/Tongan/1996 / Plasmid: modified pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q77J78
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Wsv112

Mass: 19029.248 Da / Num. of mol.: 6 / Fragment: UNP residues 1-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

White spot syndrome virus (isolate Shrimp/China/Tongan/1996)
Strain: isolate Shrimp/China/Tongan/1996 / Plasmid: modified pET30 / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q77J78

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 42.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% (w/v) PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2015 / Details: dynamically bendable toroidal mirror
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.403→47.037 Å / Num. obs: 36602 / % possible obs: 93.4 % / Redundancy: 6.7 % / B_iso Wilson estimate: 48.45 Å² / R_merge(I) obs: 0.064 / Net I/σ(I): 18.6
Reflection shell	Resolution: 2.403→2.459 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.307 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2021 / CC_1/2: 0.975 / R_pim(I) all: 0.151 / % possible all: 78.2

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Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XDS	VERSION May 1, 2016	data reduction
XDS	VERSION May 1, 2016	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3C3I

3c3i

Resolution: 2.4→33.61 Å / Cor.coef. F_o:F_c: 0.872 / Cor.coef. F_o:F_c free: 0.845 / R_factor R_free error: 0 / SU R Cruickshank DPI: 0.474 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.478 / SU R_free Blow DPI: 0.274 / SU R_free Cruickshank DPI: 0.278

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.259	1975	5.4 %	RANDOM
R_work	0.215	-	-	-
obs	0.217	36590	93.1 %	-

Displacement parameters

B_iso mean: 52.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	20.4457 Å²	0 Å²	0 Å²
2-	-	-37.2661 Å²	0 Å²
3-	-	-	16.8204 Å²

Refine analyze

Luzzati coordinate error obs: 0.37 Å

Refinement step

Cycle: 1 / Resolution: 2.4→33.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6840	0	0	150	6990

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	6978	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.17	9458	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2420	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		162	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1012	HARMONIC	5
X-RAY DIFFRACTION	t_it		6978	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.28
X-RAY DIFFRACTION	t_other_torsion	17.98
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		956	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		7425	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.4→2.47 Å / R_factor R_free error: 0 / Total num. of bins used: 18

	R_factor	Num. reflection	% reflection
R_free	0.314	240	9.92 %
R_work	0.251	2179	-
all	0.257	2419	-
obs	-	-	75.43 %

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	4.1521	-0.4874	-2.0387	0	0.1327	6.8304	0.2439	-0.0907	0.2145	-0.1216	-0.0135	0.0114	0.2316	0.4569	-0.2304	0.1445	-0.0141	-0.0495	0.2842	0.0064	0.2127	129.211	47.1945	63.6696
2	2.5406	-0.2568	-0.8602	1.0479	0.455	1.5721	0.1907	0.1203	0.0798	-0.1167	-0.1236	-0.2784	-0.0924	-0.0844	-0.0671	0.2176	-0.0375	-0.0227	0.3023	-0.0106	0.1752	117.582	52.5275	62.4413
3	13.9361	-1.0459	-6.1796	0	-1.4932	0.5537	-0.252	0.5577	-0.6815	0.1501	0.3498	-0.2178	-0.0549	-0.8228	-0.0978	0.1962	-0.0279	-0.0268	0.9111	-0.2546	0.3969	85.4967	33.263	59.6987
4	15.0041	-1.7054	0.1486	5.4256	1.838	0	-0.1913	0.0878	-0.3839	-0.0138	-0.0999	0.6175	0.1687	-1.0154	0.2911	0.2739	-0.177	0.0023	0.5264	-0.2356	0.2257	89.8269	38.8248	58.7429
5	2.2323	0.3244	0.1438	1.6847	1.2189	3.8998	0.0788	0.0251	-0.0928	-0.0685	-0.2018	0.1773	-0.1133	-0.4735	0.123	0.0394	-0.044	-0.0238	0.3456	-0.0988	0.0704	100.53	49.9938	61.9677
6	3.4275	-1.1168	4.9711	11.4315	-3.0494	10.1378	-0.0668	0.3701	0.0236	1.0091	0.2108	-0.2991	0.6299	-0.2347	-0.144	0.4499	-0.1082	0.0343	0.4992	-0.0677	0.1925	112.231	47.8961	98.7218
7	1.9412	-1.2545	2.3972	0.2266	-0.3694	4.8054	0.0075	-0.3455	-0.1242	-0.1056	-0.0816	0.0326	-0.1427	-0.1876	0.0741	0.3257	-0.1393	0.0755	0.5641	-0.029	0.1552	105.407	55.4816	87.0619
8	1.3915	0.5377	-0.1506	2.4299	0.1426	3.3858	0.0294	-0.215	0.0989	0.1947	-0.0895	0.0199	-0.2601	-0.0699	0.0601	0.1841	-0.1049	0.0186	0.3509	-0.0468	0.1341	107.941	58.527	78.2183
9	4.667	-1.806	-3.5055	0.8743	2.1452	3.7178	0.0228	-0.0912	-0.2065	-0.0131	0.211	-0.0448	0.3987	0.3305	-0.2338	0.1646	0.0048	-0.0634	0.2498	-0.0588	0.1694	126.431	39.6897	64.6423
10	9.8617	2.3718	-7.7503	1.6624	-1.5658	12.4273	0.1914	-0.0542	-0.0751	0.0435	0.2446	0.4233	1.1969	1.0206	-0.436	0.2729	0.2333	-0.0825	0.1087	-0.072	0.2716	130.404	-8.024	24.5536
11	3.1137	-0.0868	-0.7453	0.0307	0.803	3.6572	0.1279	0.0027	0.233	-0.0184	-0.0104	-0.0988	-0.17	0.2545	-0.1174	0.1453	0.0252	0.0244	-0.1007	-0.0134	0.1619	119.056	3.2778	28.0318
12	21.6572	-2.1546	-1.1921	1.1402	-4.3213	1.7853	-0.3854	0.0219	-0.2631	0.2359	0.5495	-0.1814	0.1885	-1.2282	-0.1641	0.2382	-0.1132	0.1123	0.7567	-0.2587	0.2752	85.4322	-13.9095	24.0749
13	16.1639	-6.3039	1.5619	11.0026	-2.016	1.7774	-0.5044	0.3997	-0.3726	0.4373	0.2689	0.9266	0.1849	-1.5314	0.2355	0.4487	-0.1807	0.0422	0.4505	-0.1542	0.352	89.6194	-9.0888	23.2868
14	2.6442	0.5195	-0.3428	0.0492	0.8768	4.8659	0.0565	0.2943	0.0272	-0.0448	-0.0757	0.0259	0.134	-0.5222	0.0192	0.1909	-0.0028	0.0151	0.1084	-0.0453	0.2106	100.404	1.8242	25.7941
15	13.1854	5.3969	3.0678	8.7687	-0.4222	22.1831	0.3178	0.1421	-0.5186	0.8408	0.1755	-0.3376	1.2528	-0.2488	-0.4933	0.4753	0.0675	-0.0549	0.0462	-0.0181	0.2618	111.772	-1.0588	62.8066
16	0.1978	0.9783	1.8864	6.0493	3.8399	7.1268	0.0694	-0.2654	-0.0729	0.9912	0.1381	0.0471	0.6754	-0.0796	-0.2075	0.2127	-0.0271	0.0589	0.0211	0.056	0.2266	107.181	2.8992	56.4697
17	3.2967	-1.183	1.0684	0	-0.2233	7.2696	0.0613	-0.4762	0.2116	-0.1679	0.0768	-0.2665	-0.3682	-0.0952	-0.1381	0.1292	0.011	0.0405	-0.1404	-0.0282	0.2178	107.325	9.3273	47.2799
18	2.0079	-0.2729	-0.7419	0.713	0.8993	3.4833	0.0286	-0.1636	0.1365	0.0619	0.1264	-0.0312	0.1458	0.1243	-0.1549	0.2083	-0.0391	0.0048	-0.1118	-0.0045	0.1783	114.528	3.1571	36.8195

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|3 - A\|41 }
2	X-RAY DIFFRACTION	2	{ A\|42 - A\|132 }
3	X-RAY DIFFRACTION	3	{ A\|133 - A\|150 }
4	X-RAY DIFFRACTION	4	{ B\|3 - B\|20 }
5	X-RAY DIFFRACTION	5	{ B\|21 - B\|133 }
6	X-RAY DIFFRACTION	6	{ B\|134 - B\|149 }
7	X-RAY DIFFRACTION	7	{ C\|3 - C\|46 }
8	X-RAY DIFFRACTION	8	{ C\|47 - C\|116 }
9	X-RAY DIFFRACTION	9	{ C\|117 - C\|150 }
10	X-RAY DIFFRACTION	10	{ D\|3 - D\|17 }
11	X-RAY DIFFRACTION	11	{ D\|18 - D\|135 }
12	X-RAY DIFFRACTION	12	{ D\|136 - D\|150 }
13	X-RAY DIFFRACTION	13	{ E\|3 - E\|20 }
14	X-RAY DIFFRACTION	14	{ E\|21 - E\|130 }
15	X-RAY DIFFRACTION	15	{ E\|131 - E\|149 }
16	X-RAY DIFFRACTION	16	{ F\|3 - F\|27 }
17	X-RAY DIFFRACTION	17	{ F\|28 - F\|62 }
18	X-RAY DIFFRACTION	18	{ F\|63 - F\|150 }

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