PDB-8qld: Bacteriophage T5 dUTPase mutant with loop deletion (30-35 aa)

ID or keywords:

Entry

Database: PDB / ID: 8qld

Title

Bacteriophage T5 dUTPase mutant with loop deletion (30-35 aa)

Components

Deoxyuridine 5'-triphosphate nucleotidohydrolase

Keywords

HYDROLASE / bacteriophage / T5 / dUTPase / Deoxyuridine triphosphate nucleotidohydrolases / 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

Escherichia phage T5 (virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Gabdulkhakov, A.G. / Dzhus, U.F. / Selikhanov, G.K. / Glukhov, A.S.

Funding support

Russian Federation, 1items

Citation

Journal: Int J Mol Sci / Year: 2024
Title: Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions.
Authors: Glukhov, A. / Marchenkov, V. / Dzhus, U. / Krutilina, A. / Selikhanov, G. / Gabdulkhakov, A.

History

Deposition	Sep 19, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8qld.cif.gz	216.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8qld_validation.pdf.gz	468.6 KB	Display	wwPDB validaton report
Full document	8qld_full_validation.pdf.gz	472.5 KB	Display
Data in XML	8qld_validation.xml.gz	18.2 KB	Display
Data in CIF	8qld_validation.cif.gz	25.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ql/8qld ftp://data.pdbj.org/pub/pdb/validation_reports/ql/8qld	HTTPS FTP

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Related structure data

Related structure data	8qkyC 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
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (5)

Deposited unit

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase

B: Deoxyuridine 5'-triphosphate nucleotidohydrolase

C: Deoxyuridine 5'-triphosphate nucleotidohydrolase

hetero molecules

48.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	88.726, 88.726, 99.999
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Deoxyuridine 5'-triphosphate nucleotidohydrolase Mass: 15826.225 Da / Num. of mol.: 3 / Mutation: deleted G30, T31, P33, A34, A35 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: DUT / Production host: Escherichia coli (E. coli) / References: UniProt: O48500
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.6 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.085 M HEPES sodium, 1.7% v/v Polyethylene glycol 400, 1.7 M Ammonium sulfate, 15% v/v glycerol

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Data collection

Diffraction	Mean temperature: 120 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54178 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 12, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.1→23 Å / Num. obs: 26147 / % possible obs: 99.1 % / Redundancy: 9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.094 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.1→2.16 Å / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2150 / CC_1/2: 0.954

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
CrysalisPro		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→20.001 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.922 / SU B: 12.58 / SU ML: 0.167 / Cross valid method: FREE R-VALUE / ESU R: 0.266 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2641	1160	4.679 %
R_work	0.2206	23632	-
all	0.223	-	-
obs	-	24792	94.905 %

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: 31.508 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.232 Å²	-0.116 Å²	-0 Å²
2-	-	-0.232 Å²	-0 Å²
3-	-	-	0.754 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→20.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3045	0	39	160	3244

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3151
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3040
X-RAY DIFFRACTION	r_angle_refined_deg	1.342	1.652	4250
X-RAY DIFFRACTION	r_angle_other_deg	0.461	1.576	7008
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.694	5	387
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.668	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.02	10	564
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.549	10	135
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	480
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3617
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	689
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	547
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	3062
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1508
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1693
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	192
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.068	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.186	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.144	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.21	1.598	1554
X-RAY DIFFRACTION	r_mcbond_other	1.21	1.598	1554
X-RAY DIFFRACTION	r_mcangle_it	1.938	2.85	1939
X-RAY DIFFRACTION	r_mcangle_other	1.938	2.853	1940
X-RAY DIFFRACTION	r_scbond_it	1.72	1.859	1597
X-RAY DIFFRACTION	r_scbond_other	1.561	1.831	1582
X-RAY DIFFRACTION	r_scangle_it	2.656	3.323	2311
X-RAY DIFFRACTION	r_scangle_other	2.466	3.274	2288
X-RAY DIFFRACTION	r_lrange_it	4.384	19.825	12409
X-RAY DIFFRACTION	r_lrange_other	4.302	19.634	12314

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.1-2.154	0.406	76	0.317	1746	0.321	1905	0.931	0.945	95.643	0.293
2.154-2.212	0.366	91	0.315	1662	0.318	1858	0.919	0.944	94.3488	0.285
2.212-2.276	0.38	97	0.28	1604	0.285	1815	0.917	0.957	93.719	0.247
2.276-2.345	0.348	83	0.297	1546	0.299	1746	0.93	0.953	93.299	0.257
2.345-2.42	0.449	52	0.274	1511	0.279	1691	0.913	0.958	92.4305	0.231
2.42-2.504	0.31	59	0.278	1442	0.279	1636	0.945	0.958	91.7482	0.234
2.504-2.597	0.315	68	0.268	1438	0.27	1596	0.944	0.96	94.3609	0.227
2.597-2.701	0.335	60	0.267	1387	0.27	1547	0.942	0.962	93.5359	0.217
2.701-2.819	0.256	68	0.254	1307	0.254	1455	0.964	0.965	94.5017	0.216
2.819-2.954	0.329	69	0.268	1276	0.271	1427	0.937	0.962	94.2537	0.221
2.954-3.11	0.242	60	0.218	1211	0.219	1334	0.967	0.973	95.2774	0.188
3.11-3.293	0.217	52	0.211	1181	0.211	1269	0.973	0.974	97.1631	0.189
3.293-3.514	0.264	53	0.202	1097	0.205	1208	0.96	0.975	95.1987	0.179
3.514-3.786	0.242	43	0.182	1038	0.185	1105	0.971	0.981	97.8281	0.169
3.786-4.132	0.196	43	0.167	969	0.168	1034	0.976	0.984	97.8723	0.157
4.132-4.595	0.194	57	0.149	863	0.151	951	0.976	0.987	96.7403	0.147
4.595-5.26	0.199	35	0.152	785	0.154	833	0.975	0.988	98.4394	0.151
5.26-6.334	0.227	27	0.205	695	0.206	728	0.973	0.979	99.1758	0.202
6.334-8.54	0.232	41	0.191	520	0.194	565	0.97	0.979	99.292	0.19
8.54-20.001	0.206	22	0.198	347	0.198	374	0.987	0.985	98.6631	0.197

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	0.6776	-0.1234	0.0939	2.2502	-0.1947	1.8275	-0.0128	-0.2029	0.0399	0.2006	-0.1187	0.0126	-0.249	-0.0761	0.1315	0.1983	-0.0131	-0.0318	0.0975	-0.0145	0.0135	38.5499	-2.8021	8.0839
2	1.0181	-0.0873	0.2545	2.7644	0.0172	1.4729	-0.0002	0.0819	-0.0573	-0.2703	-0.1067	-0.3966	-0.0336	0.2561	0.1069	0.1708	0.0129	0.0394	0.0587	0.034	0.0739	49.8884	-9.3897	-6.0148
3	0.9931	0.8423	-0.1021	2.081	-0.4902	1.7931	-0.0564	-0.0589	-0.0173	-0.4415	-0.0778	0.1389	0.0937	-0.3241	0.1342	0.2163	-0.0415	-0.0468	0.1266	-0.0241	0.0466	31.7475	-12.6025	-6.5205

Refinement TLS group

Selection: ALL

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