PDB-5myf: Convergent evolution involving dimeric and trimeric dUTPases in s...

ID or keywords:

Entry

Database: PDB / ID: 5myf

Title

Convergent evolution involving dimeric and trimeric dUTPases in signalling.

Components

dUTPase from DI S. aureus phage

Keywords

HYDROLASE / Staphylococcus aureus / pathogenicity island / SaPI / dUTPases / signalling / gene transfer / mobile genetic elements

Function / homology

Dimeric dUTPase Dut-like / dUTPase/dCTP pyrophosphatase / dUTPase / dUTP diphosphatase / dUTP diphosphatase activity / dUTPase from DI S. aureus phage

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Donderis, J. / Bowring, J. / Maiques, E. / Ciges-Tomas, J.R. / Alite, C. / Mehmedov, I. / Tormo-Mas, M.A. / Penades, J.R. / Marina, A.

Citation

Journal: PLoS Pathog. / Year: 2017
Title: Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization.
Authors: Donderis, J. / Bowring, J. / Maiques, E. / Ciges-Tomas, J.R. / Alite, C. / Mehmedov, I. / Tormo-Mas, M.A. / Penades, J.R. / Marina, A.

History

Deposition	Jan 26, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 6, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 17, 2024	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

-
Download

PDBx/mmCIF format	5myf.cif.gz	148.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5myf.ent.gz	117.1 KB	Display	PDB format
PDBx/mmJSON format	5myf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5myf_validation.pdf.gz	430.8 KB	Display	wwPDB validaton report
Full document	5myf_full_validation.pdf.gz	433 KB	Display
Data in XML	5myf_validation.xml.gz	14.7 KB	Display
Data in CIF	5myf_validation.cif.gz	21.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/my/5myf ftp://data.pdbj.org/pub/pdb/validation_reports/my/5myf	HTTPS FTP

-
Related structure data

Related structure data	5mydSC 5myiC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5myd-1 6ee5-d 4bqo-2 4f19-d 5ce0-1 3p1a-d 1vis-d 5mil-d 1z2o-d 1wyw-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

D: dUTPase from DI S. aureus phage

A: dUTPase from DI S. aureus phage

48.3 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)	43.642, 51.942, 148.418
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-249- HOH
2	1	A-269- HOH

#1: Protein	dUTPase from DI S. aureus phage Mass: 24156.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D0TC87*PLUS, dUTP diphosphatase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 28% PEG 6000, 0.5M LiCl2 y 0.1M Tris-HCl pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0721 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 1, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0721 Å / Relative weight: 1
Reflection	Resolution: 1.85→49.03 Å / Num. obs: 29551 / % possible obs: 99.5 % / Redundancy: 11 % / R_merge(I) obs: 0.024 / Net I/σ(I): 18.7
Reflection shell	Resolution: 1.85→1.95 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.35 / Num. unique obs: 4063 / % possible all: 96.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
REFMAC		refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5MYD

5myd

Resolution: 1.85→49.026 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.27

	R_factor	Num. reflection	% reflection
R_free	0.2186	1487	5.04 %
R_work	0.1775	-	-
obs	0.1797	29489	99.36 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.85→49.026 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2595	0	0	181	2776

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	2694
X-RAY DIFFRACTION	f_angle_d	1.521	3656
X-RAY DIFFRACTION	f_dihedral_angle_d	14.061	993
X-RAY DIFFRACTION	f_chiral_restr	0.074	400
X-RAY DIFFRACTION	f_plane_restr	0.009	476

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 (%)
1.85-1.9097	0.3131	125	0.2631	2357	X-RAY DIFFRACTION	94
1.9097-1.978	0.282	142	0.2239	2492	X-RAY DIFFRACTION	99
1.978-2.0572	0.2529	131	0.1998	2500	X-RAY DIFFRACTION	100
2.0572-2.1508	0.2209	135	0.1769	2532	X-RAY DIFFRACTION	100
2.1508-2.2642	0.2512	123	0.172	2556	X-RAY DIFFRACTION	100
2.2642-2.4061	0.2143	128	0.1738	2521	X-RAY DIFFRACTION	100
2.4061-2.5918	0.2365	140	0.1903	2557	X-RAY DIFFRACTION	100
2.5918-2.8526	0.2467	124	0.1975	2549	X-RAY DIFFRACTION	100
2.8526-3.2654	0.263	118	0.1942	2618	X-RAY DIFFRACTION	100
3.2654-4.1137	0.2084	147	0.1618	2588	X-RAY DIFFRACTION	100
4.1137-49.0435	0.1747	174	0.1542	2732	X-RAY DIFFRACTION	100

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	0.3113	-0.0791	0.2346	0.1	-0.1308	0.2143	-0.1033	0.1506	-0.0054	-0.3663	0.1568	0.4112	0.3086	-0.3554	0.0139	0.3731	-0.0753	0.0127	0.2263	-0.0299	0.2713	-26.4959	-27.8266	20.1059
2	0.3328	0.2977	-0.2265	0.2215	-0.2169	0.1495	-0.105	0.0799	0.1166	-0.2285	-0.0759	0.0816	0.2117	-0.0961	-0.0044	0.2686	0.0226	0.0124	0.1976	0.0102	0.1789	-13.0637	-16.5413	17.3022
3	0.0657	-0.0194	0.0124	0.0408	-0.0519	0.0627	0.0183	0.0168	-0.1143	-0.1194	-0.0211	0.4543	-0.0807	0.1452	0.0011	0.2475	0.0368	0.0117	0.3279	-0.0473	0.3414	-17.1503	2.3872	26.9597
4	0.1524	0.1413	-0.0528	0.099	-0.0536	0.0497	-0.0605	0.0168	0.0404	-0.2437	-0.0393	0.1589	0.1764	-0.138	0.0002	0.2766	0.0071	0.0146	0.1946	-0.0197	0.2192	-20.0164	-18.8836	19.5172
5	1.8333	-0.8658	0.1508	0.4712	-0.0847	0.1252	0.4844	-0.2816	-0.9504	0.2868	-0.2416	0.3451	-0.1116	0.3511	0.1804	0.4444	-0.1043	0.1863	0.2446	0.0464	0.0579	-18.0572	-29.7604	32.5576
6	0.0173	-0.0176	0.0464	0.189	-0.0882	0.1366	0.1528	-0.1063	0.0921	0.2097	-0.2342	0.2042	0.0758	-0.2528	-0.1022	0.598	-0.4381	0.4692	0.3908	-0.0111	0.1447	-15.9727	-9.2305	36.599
7	0.1695	0.1263	-0.0463	0.0693	-0.0418	0.0548	0.2339	-0.0937	-0.0112	0.231	-0.3184	-0.428	0.2104	0.1836	0.0003	0.3019	0.0241	-0.0158	0.3197	0.05	0.261	-5.9761	-16.6788	28.4333
8	0.1208	0.0966	-0.0117	0.0522	-0.0492	0.0747	0.0966	-0.1744	0.025	0.2573	-0.0715	0.0719	0.1604	0.1041	-0.0002	0.2808	-0.0025	0.0642	0.2334	-0.0042	0.2078	-19.3219	-19.8546	29.6816
9	0.0339	-0.0583	0.0303	0.0635	0.0065	0.0232	0.0792	0.218	0.1357	-0.1196	-0.0316	0.8053	0.2239	-0.2531	0.0015	0.2367	-0.0091	-0.0367	0.2933	-0.0102	0.4289	-28.668	-18.8663	18.0969
10	0.4542	0.0499	0.3611	0.2471	-0.1915	0.4786	0.0662	-0.0707	0.5088	-0.1187	0.1006	-0.2117	-0.3372	0.1306	-0.0158	0.2429	-0.0509	0.0528	0.1856	-0.0289	0.361	1.1763	11.3924	18.5016
11	0.336	0.0559	-0.5191	0.2995	-0.2694	0.5296	0.0395	0.0301	0.1284	-0.0345	0.0852	-0.0667	0.2224	0.0266	0.0041	0.1889	0.0041	-0.016	0.2145	0.0315	0.1871	-6.3266	-4.2351	14.6227
12	0.5057	-0.1371	0.0121	0.0659	-0.0031	0.0146	0.1598	-0.1054	0.145	-0.0426	-0.0407	-0.1973	0.042	0.3822	-0.1463	0.2094	-0.0104	0.0141	0.4933	-0.0191	0.5029	14.2225	3.9363	19.1897
13	0.305	-0.2408	0.1541	0.1796	-0.1452	0.3807	0.2797	0.093	-0.2221	-0.4006	0.1601	0.0587	0.5578	0.0382	0.0492	0.4595	0.1989	0.0154	0.4269	-0.0222	0.3686	3.3328	-13.251	13.6991
14	0.1094	-0.0237	-0.0613	0.1798	-0.1268	0.0385	-0.0061	-0.0063	0.0769	0.1643	-0.0555	-0.2656	0.2583	0.461	0.0001	0.2396	0.0407	-0.0164	0.2954	0.0157	0.2845	5.3814	-3.7831	17.8728
15	0.0576	0.0528	0.069	0.0631	-0.0055	0.0641	-0.2253	0.1147	0.279	-0.1217	0.213	0.1269	-0.2699	0.0974	0.0001	0.2462	-0.0175	0.0122	0.2367	0.0225	0.294	-2.4616	6.8782	8.3266

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 2 through 23 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 24 through 47 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 48 through 60 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 61 through 82 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 83 through 103 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 104 through 109 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 110 through 126 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 127 through 143 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 144 through 159 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 2 through 28 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 29 through 82 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 83 through 98 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 99 through 120 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 121 through 141 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 142 through 156 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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