PDB-4gv8: DUTPase from phage phi11 of S.aureus: visualization of the specie...

ID or keywords:

Entry

Database: PDB / ID: 4gv8

Title

DUTPase from phage phi11 of S.aureus: visualization of the species-specific insert

Components

DUTPase

Keywords

HYDROLASE / jelly-roll

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

Staphylococcus phage 11 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Leveles, I. / Harmat, V. / Nemeth, V. / Bendes, A. / Szabo, J. / Kadar, V. / Zagyva, I. / Rona, G. / Toth, J. / Vertessy, B.G.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure and enzymatic mechanism of a moonlighting dUTPase
Authors: Leveles, I. / Nemeth, V. / Szabo, J.E. / Harmat, V. / Nyiri, K. / Bendes, A.A. / Papp-Kadar, V. / Zagyva, I. / Rona, G. / Ozohanics, O. / Vekey, K. / Toth, J. / Vertessy, B.G.

History

Deposition	Aug 30, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 8, 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 / struct_conn / struct_ncs_dom_lim / struct_site 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4gv8.cif.gz	373.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4gv8_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gv/4gv8 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/4gv8	HTTPS FTP

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Related structure data

Related structure data	2py4S S: Starting model for refinement
Similar structure data	1d4a-1 5eai-1 4wrk-1 5ojj-1 2f1o-1 4wrk-2 5eai-2 3zf1-1 6llc-4 1kbo-2 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: DUTPase

B: DUTPase

C: DUTPase

D: DUTPase

E: DUTPase

F: DUTPase

hetero molecules

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

1

A: DUTPase

B: DUTPase

C: DUTPase

hetero molecules

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

2

D: DUTPase

E: DUTPase

F: DUTPase

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.660, 109.660, 169.270
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

Components on special symmetry positions

ID	Model	Components
1	1	D-336- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	D
2	2	E
3	2	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	ARG	ARG	3	A	A	4 - 19	4 - 19
2	1	1	THR	THR	ARG	ARG	3	B	B	4 - 19	4 - 19
3	1	1	THR	THR	ARG	ARG	3	C	C	4 - 19	4 - 19
1	2	1	ASP	ASP	ALA	ALA	3	A	A	24 - 82	24 - 82
2	2	1	ASP	ASP	ALA	ALA	3	B	B	24 - 82	24 - 82
3	2	1	ASP	ASP	ALA	ALA	3	C	C	24 - 82	24 - 82
1	3	1	HIS	HIS	ILE	ILE	3	A	A	85 - 97	85 - 97
2	3	1	HIS	HIS	ILE	ILE	3	B	B	85 - 97	85 - 97
3	3	1	HIS	HIS	ILE	ILE	3	C	C	85 - 97	85 - 97
1	4	1	GLY	GLY	GLU	GLU	4	A	A	101 - 154	101 - 154
2	4	1	GLY	GLY	GLU	GLU	4	B	B	101 - 154	101 - 154
3	4	1	GLY	GLY	GLU	GLU	4	C	C	101 - 154	101 - 154
1	5	1	DUP	DUP	MG	MG	4	A	G - I	201 - 202
2	5	1	DUP	DUP	MG	MG	4	B	J - K	201 - 202
3	5	1	DUP	DUP	MG	MG	4	C	L - M	201 - 202
1	1	2	THR	THR	ARG	ARG	3	D	D	4 - 19	4 - 19
2	1	2	THR	THR	ARG	ARG	3	E	E	4 - 19	4 - 19
3	1	2	THR	THR	ARG	ARG	3	F	F	4 - 19	4 - 19
1	2	2	ASP	ASP	ALA	ALA	3	D	D	24 - 82	24 - 82
2	2	2	ASP	ASP	ALA	ALA	3	E	E	24 - 82	24 - 82
3	2	2	ASP	ASP	ALA	ALA	3	F	F	24 - 82	24 - 82
1	3	2	HIS	HIS	ILE	ILE	3	D	D	85 - 97	85 - 97
2	3	2	HIS	HIS	ILE	ILE	3	E	E	85 - 97	85 - 97
3	3	2	HIS	HIS	ILE	ILE	3	F	F	85 - 97	85 - 97
1	4	2	GLY	GLY	GLU	GLU	4	D	D	101 - 154	101 - 154
2	4	2	GLY	GLY	GLU	GLU	4	E	E	101 - 154	101 - 154
3	4	2	GLY	GLY	GLU	GLU	4	F	F	101 - 154	101 - 154
1	5	2	DUP	DUP	MG	MG	4	D	N - P	201 - 202
2	5	2	DUP	DUP	MG	MG	4	E	Q - R	201 - 202
3	5	2	DUP	DUP	MG	MG	4	F	S - T	201 - 202

NCS ensembles :

ID
1
2

#1: Protein	DUTPase Mass: 18387.584 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage 11 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SDV3, dUTP diphosphatase
#2: Chemical	ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE Mass: 467.157 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₃P₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.31 Å³/Da / Density % sol: 46.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% MPD, 0.02M calcium chloride, 0.1M sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 30, 2012 / Details: MIRRORS

Radiation

Monochromator: Fixed exit double / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.1→47.104 Å / Num. obs: 60917 / Observed criterion σ(I): -3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID
2.1-2.15	12.8	0.978	3.07	1
2.15-47.1	13.3	0.058	34.37	1

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Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.5.0110	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PY4

2py4

Resolution: 2.1→47.1 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.947 / SU B: 11.689 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23224	3140	5.2 %	RANDOM
R_work	0.18303	-	-	-
obs	0.1858	57719	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 50.655 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.26 Å²	-0 Å²	-0 Å²
2-	-	0.26 Å²	0 Å²
3-	-	-	-0.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→47.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6786	0	176	376	7338

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.02	7081
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4432
X-RAY DIFFRACTION	r_angle_refined_deg	1.888	1.988	9687
X-RAY DIFFRACTION	r_angle_other_deg	1.024	3	10922
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.972	5	914
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.156	25.317	284
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.586	15	1067
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.962	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1147
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	7892
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1304
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.036	1.5	4554
X-RAY DIFFRACTION	r_mcbond_other	0.363	1.5	1878
X-RAY DIFFRACTION	r_mcangle_it	1.677	2	7298
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.618	3	2527
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.765	4.5	2387
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	516	tight positional	0.13	0.05
1	1	B	516	tight positional	0.14	0.05
1	1	C	516	tight positional	0.12	0.05
2	2	D	516	tight positional	0.17	0.05
2	2	E	516	tight positional	0.15	0.05
2	2	F	516	tight positional	0.18	0.05
1	1	A	678	medium positional	0.26	0.5
1	1	B	678	medium positional	0.33	0.5
1	1	C	678	medium positional	0.27	0.5
2	2	D	659	medium positional	0.35	0.5
2	2	E	659	medium positional	0.28	0.5
2	2	F	659	medium positional	0.27	0.5
1	1	A	558	loose positional	0.56	5
1	1	B	558	loose positional	0.42	5
1	1	C	558	loose positional	0.37	5
2	2	D	516	loose positional	0.36	5
2	2	E	516	loose positional	0.26	5
2	2	F	516	loose positional	0.32	5
1	1	A	516	tight thermal	0.95	0.5
1	1	B	516	tight thermal	0.85	0.5
1	1	C	516	tight thermal	0.87	0.5
2	2	D	516	tight thermal	0.65	0.5
2	2	E	516	tight thermal	0.7	0.5
2	2	F	516	tight thermal	0.76	0.5
1	1	A	678	medium thermal	1.07	2
1	1	B	678	medium thermal	1.04	2
1	1	C	678	medium thermal	1.03	2
2	2	D	659	medium thermal	0.84	2
2	2	E	659	medium thermal	0.82	2
2	2	F	659	medium thermal	0.72	2
1	1	A	558	loose thermal	1.23	10
1	1	B	558	loose thermal	1.08	10
1	1	C	558	loose thermal	1.15	10
2	2	D	516	loose thermal	0.85	10
2	2	E	516	loose thermal	0.9	10
2	2	F	516	loose thermal	0.95	10

LS refinement shell

Resolution: 2.1→2.155 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.131	1	-
R_work	0.321	4099	-
obs	-	-	99.98 %

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	0.2046	0.1674	0.0007	0.671	-0.3683	0.8546	0.0494	0.1089	-0.0302	-0.0402	0.072	0.0365	0.0959	-0.0504	-0.1214	0.1228	-0.003	-0.0233	0.1958	0.009	0.1419	28.2875	39.3742	-10.7441
2	0.456	0.1388	-0.137	0.3697	-0.4695	1.0639	0.0176	0.0103	0.0809	0.055	0.0247	0.0831	-0.06	-0.1444	-0.0422	0.0911	0.0391	0.0042	0.1992	0.0546	0.171	17.0552	55.2423	5.1133
3	0.2557	-0.0529	0.1082	0.909	-0.5379	0.6562	0.0177	0.0295	0.0093	0.0242	0.0131	-0.0394	-0.0183	0.1015	-0.0307	0.1358	0.0106	-0.0121	0.1674	0.0093	0.1363	41.9724	52.543	5.5986
4	0.7762	1.1496	-0.5475	1.8861	-0.569	0.8221	-0.1779	0.0128	-0.2401	-0.0969	0.1562	-0.3342	0.4196	0.3287	0.0218	0.2411	0.2302	-0.0448	0.3282	-0.2203	0.3351	3.6063	14.4147	-32.4704
5	2.2436	0.0658	0.1289	0.3027	0.2969	0.663	-0.1066	0.323	-0.0237	-0.1077	0.2502	0.0172	-0.0106	0.316	-0.1435	0.1401	-0.0726	-0.0113	0.4216	-0.1182	0.1533	-5.2333	32.3116	-47.5251
6	0.8085	0.0904	-0.1985	0.5267	0.5913	0.7881	-0.0676	-0.0103	-0.1039	-0.0132	0.206	-0.1138	0.0063	0.2747	-0.1384	0.0057	0.0086	0.0126	0.3722	-0.1334	0.1626	5.6345	38.5196	-25.8606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 141
2	X-RAY DIFFRACTION	1	B	142 - 164
3	X-RAY DIFFRACTION	1	A	201 - 202
4	X-RAY DIFFRACTION	2	B	3 - 141
5	X-RAY DIFFRACTION	2	C	142 - 164
6	X-RAY DIFFRACTION	2	B	201 - 202
7	X-RAY DIFFRACTION	3	C	2 - 141
8	X-RAY DIFFRACTION	3	A	142 - 155
9	X-RAY DIFFRACTION	3	C	201 - 202
10	X-RAY DIFFRACTION	4	D	3 - 141
11	X-RAY DIFFRACTION	4	E	142 - 164
12	X-RAY DIFFRACTION	4	D	201 - 202
13	X-RAY DIFFRACTION	5	E	2 - 141
14	X-RAY DIFFRACTION	5	F	142 - 164
15	X-RAY DIFFRACTION	5	E	201 - 202
16	X-RAY DIFFRACTION	6	F	3 - 141
17	X-RAY DIFFRACTION	6	D	142 - 154
18	X-RAY DIFFRACTION	6	F	201 - 202

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi