PDB-6dre: ADP-ribosyltransferase toxin/immunity pair

ID or keywords:

Entry

Database: PDB / ID: 6dre

Title

ADP-ribosyltransferase toxin/immunity pair

Components

ADP-ribosyl-(Dinitrogen reductase) hydrolase
PAAR repeat-containing protein

Keywords

TOXIN / Immunity / Type VI secretion / ADP ribosyl transferase

Function / homology

Function and homology information

[protein ADP-ribosylarginine] hydrolase / ADP-ribosylarginine hydrolase activity / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / host cell cytoplasm / extracellular region / metal ion binding
Similarity search - Function

Biological species

Serratia proteamaculans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Bosch, D.E. / Ting, S. / Allaire, M. / Mougous, J.D.

Citation

Journal: Cell / Year: 2018
Title: Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins.
Authors: Ting, S.Y. / Bosch, D.E. / Mangiameli, S.M. / Radey, M.C. / Huang, S. / Park, Y.J. / Kelly, K.A. / Filip, S.K. / Goo, Y.A. / Eng, J.K. / Allaire, M. / Veesler, D. / Wiggins, P.A. / Peterson, S.B. / Mougous, J.D.

History

Deposition	Jun 11, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6dre.cif.gz	229.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6dre.ent.gz	192.6 KB	Display	PDB format
PDBx/mmJSON format	6dre.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6dre_validation.pdf.gz	429.9 KB	Display	wwPDB validaton report
Full document	6dre_full_validation.pdf.gz	432.2 KB	Display
Data in XML	6dre_validation.xml.gz	26.3 KB	Display
Data in CIF	6dre_validation.cif.gz	40.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/6dre ftp://data.pdbj.org/pub/pdb/validation_reports/dr/6dre	HTTPS FTP

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Related structure data

Related structure data	6drhC C: citing same article (ref.)
Similar structure data	4tvz-1 5z3k-1 3py6-1 6n4n-1 3md7-1 2taa-2 6qnm-d 2yxl-d 6l3n-1 2ggq-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ADP-ribosyl-(Dinitrogen reductase) hydrolase

B: PAAR repeat-containing protein

hetero molecules

60.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	136.355, 51.036, 94.899
Angle α, β, γ (deg.)	90.000, 123.710, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	ADP-ribosyl-(Dinitrogen reductase) hydrolase Mass: 41399.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia proteamaculans (bacteria) / Strain: 568 / Gene: Spro_3018 / Production host: Escherichia coli (E. coli) References: UniProt: A8GG79, ADP-ribosyl-[dinitrogen reductase] hydrolase
#2: Protein	PAAR repeat-containing protein Mass: 18858.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia proteamaculans (strain 568) (bacteria) Strain: 568 / Gene: Spro_3017 / Production host: Escherichia coli (E. coli) / References: UniProt: A8GG78
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.29 Å³/Da / Density % sol: 46.36 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Na2HPO4, 1.6 M citric acid pH 4.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 5, 2017
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.8→67 Å / Num. obs: 95211 / % possible obs: 97.3 % / Redundancy: 6.4 % / B_iso Wilson estimate: 18.1 Å² / R_merge(I) obs: 0.045 / Net I/av σ(I): 33.2 / Net I/σ(I): 33.2
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.391 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1081 / % possible all: 93

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing
PDB_EXTRACT	3.22	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.8→66.899 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.18

	R_factor	Num. reflection	% reflection
R_free	0.1946	3866	4.06 %
R_work	0.1509	-	-
obs	0.1527	95211	96.52 %

Solvent computation

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

Displacement parameters

B_iso max: 88.52 Å² / B_iso mean: 24.8286 Å² / B_iso min: 10.07 Å²

Refinement step

Cycle: final / Resolution: 1.8→66.899 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4185	0	1	599	4785
B_iso mean	-	-	22.73	34.21	-
Num. residues	-	-	-	-	535

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4284
X-RAY DIFFRACTION	f_angle_d	1.081	5822
X-RAY DIFFRACTION	f_chiral_restr	0.061	636
X-RAY DIFFRACTION	f_plane_restr	0.007	771
X-RAY DIFFRACTION	f_dihedral_angle_d	2.875	3265

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.822	0.2828	133	0.2231	3165	3298	93
1.822-1.845	0.2365	134	0.206	3094	3228	94
1.845-1.8693	0.1943	135	0.1943	3260	3395	95
1.8693-1.8949	0.2817	138	0.2067	3192	3330	95
1.8949-1.922	0.2436	136	0.1928	3235	3371	95
1.922-1.9507	0.2313	136	0.1841	3202	3338	95
1.9507-1.9812	0.2267	138	0.1722	3249	3387	96
1.9812-2.0137	0.2058	138	0.1766	3258	3396	96
2.0137-2.0484	0.2015	138	0.1617	3233	3371	96
2.0484-2.0856	0.2178	136	0.1554	3209	3345	96
2.0856-2.1258	0.1939	138	0.1515	3288	3426	96
2.1258-2.1692	0.2229	136	0.1442	3213	3349	96
2.1692-2.2163	0.2194	140	0.1472	3332	3472	96
2.2163-2.2679	0.1856	137	0.1543	3183	3320	96
2.2679-2.3246	0.2347	137	0.1631	3278	3415	96
2.3246-2.3875	0.2066	134	0.1525	3235	3369	97
2.3875-2.4577	0.237	137	0.1586	3272	3409	97
2.4577-2.537	0.2226	138	0.1542	3302	3440	97
2.537-2.6277	0.212	140	0.1501	3284	3424	97
2.6277-2.7329	0.1901	137	0.1562	3267	3404	97
2.7329-2.8573	0.1835	140	0.1583	3281	3421	97
2.8573-3.008	0.2297	144	0.1651	3368	3512	98
3.008-3.1964	0.21	138	0.1614	3271	3409	98
3.1964-3.4432	0.1705	140	0.143	3299	3439	98
3.4432-3.7897	0.1869	140	0.1299	3320	3460	99
3.7897-4.338	0.1551	143	0.1183	3348	3491	99
4.338-5.465	0.1378	140	0.1213	3346	3486	99
5.465-66.9448	0.1659	145	0.148	3361	3506	99

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	1.6287	1.159	-1.6243	3.3533	1.7758	7.3809	0.1902	0.0353	0.1896	-0.0933	-0.1036	0.2146	-0.6733	-0.8956	-0.0747	0.2108	0.0639	0.0089	0.292	0.0015	0.1938	30.1602	50.3808	27.264
2	3.5852	1.8256	-4.7318	3.9558	-2.0444	6.2744	0.0824	0.1247	0.1947	-0.0048	-0.0222	0.3128	-0.1742	-0.3599	-0.0223	0.1983	-0.0198	-0.0194	0.3383	-0.046	0.2197	13.0144	36.3981	18.9549
3	0.9054	-0.0394	-0.4041	0.1643	-0.0269	1.4772	-0.0589	0.3765	0.0303	-0.0468	0.0039	-0.0081	-0.0265	-0.1082	0.0463	0.1792	-0.0153	-0	0.06	0.0277	0.159	39.0923	38.1369	8.7787
4	2.5223	-0.8999	-1.1311	3.409	2.2453	2.9387	-0.1254	-0.1956	-0.0138	0.0589	0.1712	-0.0908	-0.0056	0.337	-0.0577	0.1049	-0.023	-0.0206	0.1993	0.0434	0.1531	63.9083	41.3342	26.2242
5	1.7954	0.103	0.2701	1.8055	-0.0793	3.893	0.0988	-0.0932	-0.4583	0.0583	-0.0314	-0.2097	0.3993	0.069	-0.0355	0.1792	-0.0051	0.01	0.0873	0.0416	0.2196	50.1561	22.1124	18.5943
6	6.1627	2.9623	-4.0101	3.2965	-1.19	3.7777	0.0614	-0.8976	-0.5204	0.2555	-0.1705	-0.0956	0.1232	0.4561	0.1062	0.2027	0.0069	-0.0357	0.2588	0.1157	0.2186	52.8998	22.9673	28.4014
7	0.9839	0.1059	0.0372	0.3467	0.0497	1.1891	-0.018	0.0333	0.052	-0.0389	-0.0278	-0.0083	-0.0392	-0.0098	0.049	0.133	-0.02	-0.003	0.094	0.0206	0.1389	45.9589	39.312	16.1057
8	7.7681	5.0218	0.7727	7.9584	-0.2145	3.1151	-0.0886	0.3208	-0.4153	-0.1614	0.086	-0.0563	0.3087	-0.292	0.0029	0.2045	-0.0573	0.0116	0.1886	-0.059	0.1231	22.8499	17.9533	12.6505
9	2.39	0.0761	-1.3623	2.3064	-0.0489	1.2343	-0.0362	-0.0553	-0.4051	0.0398	-0.093	0.0271	0.2395	-0.1574	0.1403	0.1903	-0.0678	-0.0004	0.2003	-0.0266	0.1491	24.6728	18.5283	20.125
10	9.4576	2.5454	-7.6945	3.7064	-3.4713	8.4707	-0.0029	0.2153	0.1606	-0.0247	0.1143	0.1327	0.1052	-0.2911	-0.1101	0.1365	-0.0701	-0.0294	0.2106	-0.0111	0.1692	7.0763	24.8349	24.4955
11	2.0275	0.1559	-0.2072	2.829	-0.537	1.035	-0.0437	-0.1459	-0.1967	0.1064	0.0053	-0.0416	0.1026	-0.0628	0.0604	0.1554	-0.0446	0.0266	0.2507	-0.0107	0.1	20.0477	24.8871	27.8103
12	7.8504	0.8935	6.2583	0.4542	0.8183	5.0295	-0.152	-0.5959	0.1098	-0.0175	-0.1487	0.5612	-0.1677	-1.1325	0.2403	0.1673	0.0212	0.0024	0.3756	-0.0583	0.318	8.7629	43.7674	36.1437
13	0.2157	-0.1356	-0.7622	0.0739	0.4451	2.6217	0.2706	-0.3906	0.2204	0.2626	-0.3567	0.1587	-0.3365	-0.0345	0.0226	0.2723	-0.1088	0.0133	0.3312	-0.0847	0.2035	15.6882	32.3937	31.4663
14	1.1975	-0.8144	-1.2853	2.187	2.2509	3.4833	-0.0714	-0.0055	0.0683	-0.0876	0.0147	0.0576	-0.0792	-0.0746	0.0476	0.0918	-0.0379	-0.019	0.1711	-0.0206	0.135	21.7493	35.436	26.858
15	7.0137	-1.47	1.7926	3.7854	-4.9268	6.4902	-0.2044	0.2063	0.4596	0.1016	0.0865	0.0191	-0.3778	0.1195	0.1197	0.2467	-0.0124	-0.0518	0.2408	-0.0635	0.152	19.2607	44.4414	33.8723

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 21 )	A	2 - 21
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 39 )	A	22 - 39
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 89 )	A	40 - 89
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 90 through 116 )	A	90 - 116
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 117 through 150 )	A	117 - 150
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 151 through 176 )	A	151 - 176
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 177 through 366 )	A	177 - 366
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 4 through 19 )	B	4 - 19
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 20 through 39 )	B	20 - 39
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 58 )	B	40 - 58
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 59 through 86 )	B	59 - 86
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 87 through 100 )	B	87 - 100
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 101 through 111 )	B	101 - 111
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 112 through 158 )	B	112 - 158
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 159 through 172 )	B	159 - 172

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