PDB-5y5p: Crystal structure of the dUTPase of white spot syndrome virus in ...

ID or keywords:

Entry

Database: PDB / ID: 5y5p

Title

Crystal structure of the dUTPase of white spot syndrome virus in complex with dU,PPi and Mg2+

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: 2.03 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 ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5y5p.cif.gz	404.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5y5p.ent.gz	330 KB	Display	PDB format
PDBx/mmJSON format	5y5p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5y5p_validation.pdf.gz	5.4 MB	Display	wwPDB validaton report
Full document	5y5p_full_validation.pdf.gz	5.4 MB	Display
Data in XML	5y5p_validation.xml.gz	40.1 KB	Display
Data in CIF	5y5p_validation.cif.gz	56.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y5/5y5p ftp://data.pdbj.org/pub/pdb/validation_reports/y5/5y5p	HTTPS FTP

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Related structure data

Related structure data	5y5oSC 5y5qC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1rqe-d 1dwa-d 1dwi-d 1dwj-d 6jkc-d 3k9v-1 3etc-2 5nau-d 6jkd-d 1e71-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) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (5)
#151 - Jul 2012
Hypoxanthine-guanine phosphoribosyltransferase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#116 - Aug 2009
Sulfotransferases
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)

Deposited unit

A: Wsv112

B: Wsv112

C: Wsv112

D: Wsv112

E: Wsv112

F: Wsv112

hetero molecules

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

1

A: Wsv112

B: Wsv112

C: Wsv112

hetero molecules

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

2

D: Wsv112

E: Wsv112

F: Wsv112

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.129, 57.266, 110.795
Angle α, β, γ (deg.)	90.00, 95.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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: Chemical	ChemComp-DUR / 2'-DEOXYURIDINE Mass: 228.202 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₉H₁₂N₂O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H₂O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.44 Å³/Da / Density % sol: 49.52 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 0.1 M Tris HCl pH 8.1, 28% (w/v) PEG 3350,0.2 M sodium acetate

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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: Oct 4, 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: 2.026→87.698 Å / Num. obs: 71757 / % possible obs: 99.7 % / Redundancy: 7.3 % / B_iso Wilson estimate: 32.79 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.034 / Net I/σ(I): 15.9
Reflection shell	Resolution: 2.026→2.043 Å / Redundancy: 7 % / R_merge(I) obs: 0.828 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1805 / CC_1/2: 0.872 / R_pim(I) all: 0.339 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
autoPROC	1.0.4	data reduction
autoPROC	1.0.4	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5Y5O

5y5o

Resolution: 2.03→40.6 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.935 / R_factor R_free error: 0 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU R_free Blow DPI: 0.15 / SU R_free Cruickshank DPI: 0.15

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.219	3503	4.94 %	thin shells
R_work	0.194	-	-	-
obs	0.195	70931	99.2 %	-

Displacement parameters

B_iso mean: 41.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.6652 Å²	0 Å²	1.3328 Å²
2-	-	-9.2534 Å²	0 Å²
3-	-	-	0.5883 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: 1 / Resolution: 2.03→40.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7543	0	145	436	8124

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	7827	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.06	10604	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2749	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		191	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1173	HARMONIC	5
X-RAY DIFFRACTION	t_it		7827	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		2	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	3.55
X-RAY DIFFRACTION	t_other_torsion	15.57
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1062	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		8981	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.03→2.08 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.245	206	3.99 %
R_work	0.307	4956	-
all	0.305	5162	-
obs	-	-	98.54 %

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	3.9361	-2.1824	-1.581	0.7347	0.47	5.6882	-0.0452	-0.0734	-1.1951	-0.162	-0.1061	0.3527	0.6622	0.0255	0.1513	0.3743	-0.0508	0.0734	0.0477	0.0124	0.594	-17.4691	-33.4671	-43.4734
2	2.3647	-0.0926	0.0379	0.8823	0.1203	2.0431	0.0481	0.1126	-0.4158	0.0001	-0.0224	0.2694	0.292	-0.2558	-0.0257	0.1131	-0.0465	0.0548	0.0597	-0.0012	0.2187	-22.3073	-18.7598	-43.0741
3	1.7603	4.7635	-1.8349	11.2011	-2.1737	2.2623	0.074	-0.1203	-0.0042	0.363	-0.154	-0.3077	-0.324	0.4455	0.0801	0.1783	-0.0837	0.0353	0.408	0.0946	0.155	11.205	1.4272	-45.9557
4	6.2366	0.7919	1.1475	0.7089	-0.7855	1.4792	0.1316	-0.0494	-0.4032	0.0863	-0.0164	0.0953	0.1854	0.0304	-0.1152	0.1453	-0.0008	0.0624	0.0468	0.0184	0.1062	-1.3525	-16.847	-33.3959
5	6.0326	2.481	1.1273	2.1778	1.256	4.139	0.0443	0.3263	0.2476	0.3782	-0.1723	0.0363	-0.1281	0.791	0.128	0.2463	-0.0902	0.0598	0.4411	0.1098	0.1424	6.2166	-0.186	-43.169
6	1.2337	0.1885	1.2066	0.6373	-0.0429	1.8074	0.0321	0.1607	0.0301	0.0097	-0.0756	0.0669	-0.175	0.1176	0.0435	0.1365	-0.0065	0.0747	0.1254	0.0224	0.086	-10.0845	-3.3611	-42.5822
7	7.6627	-2.2802	6.0087	5.6604	-2.9171	10.0038	0.1727	0.1606	-0.1631	-0.6349	0.0434	0.662	1.0108	-0.3602	-0.2161	0.2812	-0.0148	-0.0083	0.2859	-0.0021	0.0644	-25.1488	-6.5829	-77.8615
8	1.1055	-3.103	-5.2073	7.2886	2.1878	-1.0449	0.2888	0.3688	-0.2025	0.2589	-0.4597	0.0385	-0.5671	0.295	0.1709	0.336	-0.0925	0.0317	0.6736	0.1807	0.2875	-9.5041	7.6442	-60.9404
9	2.074	-3.6499	6.8181	3.0358	-6.7691	3.308	0.1791	0.6166	-0.3127	-0.5689	-0.0735	0.2009	0.4405	0.2342	-0.1056	0.216	0.071	0.0188	0.333	-0.0793	0.1358	-16.0896	-9.8681	-70.5135
10	1.3875	-0.1102	0.9262	0.8306	-0.4121	2.6739	0.001	0.2627	0.0708	-0.0263	0.0199	0.1758	-0.07	-0.126	-0.021	0.1071	0.023	0.0607	0.1597	0.0336	0.1323	-24.4326	-2.2206	-57.7057
11	2.3821	-0.6714	0.0669	1.1826	-0.2012	2.3227	0.1111	0.168	-0.2684	-0.1122	-0.0614	0.1506	0.2008	-0.0539	-0.0497	0.1297	-0.0189	0.0228	0.0902	-0.0546	0.1645	-18.5097	-15.4486	-49.2587
12	3.2812	2.5703	0.3149	9.8843	-1.7446	0.0302	-0.3105	0.5582	-0.5901	-0.167	0.0741	0.2912	0.1588	-0.3839	0.2364	0.6216	-0.0623	-0.1346	0.1369	-0.0941	0.5445	-17.4562	-37.9277	-50.6243
13	6.8887	3.264	-6.4239	8.6469	-7.6292	9.9638	-0.3877	-0.1396	-0.7935	-0.38	0.1601	0.1255	0.8967	0.0949	0.2277	0.2095	0.0186	0.0965	0.2392	-0.027	0.2706	31.2074	-23.9421	-21.5026
14	2.2424	-0.425	-0.1643	0.4272	0.0401	1.0074	0.0238	-0.2487	0.1401	0.0145	0.06	-0.2052	-0.0763	0.2372	-0.0838	0.1247	-0.0328	0.0751	0.2011	-0.0396	0.0835	29.0001	-6.8104	-18.9218
15	19.9638	0.7418	-0.9356	10.7561	-1.8174	0.0536	0.223	-0.1198	-0.502	0.8598	-0.2608	0.5704	0.2157	-0.9002	0.0378	0.1316	-0.0855	0.079	0.2824	0.119	0.1365	-9.7587	-16.0038	-12.0166
16	3.744	0.7547	-0.3049	0.7052	-0.389	0.4074	0.0224	0.3319	-0.2801	-0.0092	0.0217	-0.0014	0.0582	0.0737	-0.0441	0.1777	-0.0178	0.0731	0.1746	0.0082	0.1191	11.2457	-12.8816	-29.8202
17	3.915	-1.0102	0.5128	4.0495	-2.0359	1.0935	-0.0048	-0.6607	-0.4216	-0.0931	0.332	0.5862	0.1093	-0.2283	-0.3272	0.2148	-0.0817	0.039	0.374	0.135	0.1747	-3.0156	-13.3353	-14.8487
18	1.6441	-0.3015	0.3102	1.1153	-0.2607	1.0641	0.0239	-0.3007	0.1004	0.0772	0.066	-0.0156	-0.0481	-0.0609	-0.0899	0.1072	-0.0279	0.0887	0.1279	-0.0017	0.0201	9.5279	-4.3503	-16.4426
19	2.4545	-0.4844	0.5236	1.2989	-0.0578	1.3057	-0.0862	-0.6744	0.0666	0.1798	0.2181	-0.1448	-0.0027	-0.0187	-0.1319	0.1478	0.0174	0.065	0.3121	-0.0199	0.0153	16.5712	-6.5537	-5.2932
20	8.7932	1.3309	-0.3144	2.1543	0.0917	-0.1464	-0.3176	0.0554	-0.0296	0.2647	0.2227	0.277	-0.127	0.5022	0.0949	0.2152	0.0327	0.0757	0.6311	0.1258	0.057	9.7689	-19.6299	12.9209
21	4.959	0.2456	4.8355	6.1972	1.9488	8.2102	-0.2145	-0.9777	-0.2189	1.2941	0.3113	-0.3418	0.3995	0.2987	-0.0968	0.2212	0.0648	-0.0035	0.7933	0.0078	-0.0098	27.8068	-11.2823	12.9279
22	2.3706	-0.5837	0.1148	1.5876	0.4427	1.6009	0.0244	-0.7472	0.2432	0.1223	0.0426	-0.1998	-0.04	0.0807	-0.067	0.1389	0.0122	0.0255	0.4916	-0.0811	0.0296	23.3471	-3.7855	1.6922
23	1.8692	-0.346	-0.3335	1.0296	1.0399	1.5307	-0.0042	-0.3322	0.0449	0.0494	0.1086	-0.0764	-0.0285	0.172	-0.1044	0.125	0.0129	0.0279	0.2256	-0.0107	0.0217	28.5507	-10.2275	-13.0285
24	0.5248	-0.5588	-2.8156	0	-1.2458	3.4759	-0.2893	-0.4446	0.2881	-0.1443	0.1643	-0.4482	0.3495	0.3258	0.125	0.0321	0.0084	-0.0053	0.5416	-0.1301	0.1028	42.2828	-10.4358	-6.6433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|2 - A\|21 }
2	X-RAY DIFFRACTION	2	{ A\|22 - A\|128 }
3	X-RAY DIFFRACTION	3	{ A\|129 - A\|148 }
4	X-RAY DIFFRACTION	4	{ A\|149 - A\|171 }
5	X-RAY DIFFRACTION	5	{ B\|3 - B\|19 }
6	X-RAY DIFFRACTION	6	{ B\|20 - B\|135 }
7	X-RAY DIFFRACTION	7	{ B\|136 - B\|149 }
8	X-RAY DIFFRACTION	8	{ B\|150 - B\|169 }
9	X-RAY DIFFRACTION	9	{ C\|2 - C\|11 }
10	X-RAY DIFFRACTION	10	{ C\|12 - C\|103 }
11	X-RAY DIFFRACTION	11	{ C\|104 - C\|142 }
12	X-RAY DIFFRACTION	12	{ C\|143 - C\|150 }
13	X-RAY DIFFRACTION	13	{ D\|1 - D\|11 }
14	X-RAY DIFFRACTION	14	{ D\|12 - D\|135 }
15	X-RAY DIFFRACTION	15	{ D\|136 - D\|148 }
16	X-RAY DIFFRACTION	16	{ D\|149 - D\|171 }
17	X-RAY DIFFRACTION	17	{ E\|3 - E\|19 }
18	X-RAY DIFFRACTION	18	{ E\|20 - E\|87 }
19	X-RAY DIFFRACTION	19	{ E\|88 - E\|143 }
20	X-RAY DIFFRACTION	20	{ E\|144 - E\|158 }
21	X-RAY DIFFRACTION	21	{ F\|3 - F\|20 }
22	X-RAY DIFFRACTION	22	{ F\|21 - F\|98 }
23	X-RAY DIFFRACTION	23	{ F\|99 - F\|152 }
24	X-RAY DIFFRACTION	24	{ F\|153 - F\|169 }

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About Yorodumi

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Yorodumi