PDB-8ux2: Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in com...

ID or keywords:

Entry

Database: PDB / ID: 8ux2

Title

Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+

Components

NAD(+)--protein-threonine ADP-ribosyltransferase

Keywords

TRANSFERASE / mono-ADP-ribosyltransferase / ADP-ribosylation / bacterial effector

Function / homology

glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / host cell / extracellular region / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(+)--protein-threonine ADP-ribosyltransferase

Function and homology information

Biological species

Chromobacterium violaceum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.87 Å

Authors

Zhang, Z. / Rondon, H. / Das, C.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM126296	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R21AI171709	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	T32AI148103	United States

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Crystal structure of bacterial ubiquitin ADP-ribosyltransferase CteC reveals a substrate-recruiting insertion.
Authors: Zhang, Z. / Rondon-Cordero, H.M. / Das, C.

History

Deposition	Nov 8, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ux2.cif.gz	300.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ux2.ent.gz	244 KB	Display	PDB format
PDBx/mmJSON format	8ux2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ux2_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8ux2_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8ux2_validation.xml.gz	31.9 KB	Display
Data in CIF	8ux2_validation.cif.gz	46 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/8ux2 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/8ux2	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NAD(+)--protein-threonine ADP-ribosyltransferase

B: NAD(+)--protein-threonine ADP-ribosyltransferase

C: NAD(+)--protein-threonine ADP-ribosyltransferase

hetero molecules

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

1

A: NAD(+)--protein-threonine ADP-ribosyltransferase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NAD(+)--protein-threonine ADP-ribosyltransferase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: NAD(+)--protein-threonine ADP-ribosyltransferase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.656, 82.937, 151.212
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NAD(+)--protein-threonine ADP-ribosyltransferase Mass: 27580.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: cteC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7NY09
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25M calcium acetate, 20% PEG 3000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.87→41.47 Å / Num. obs: 60539 / % possible obs: 99.81 % / Redundancy: 11.5 % / CC_1/2: 0.978 / Net I/σ(I): 22.18
Reflection shell	Resolution: 1.87→1.938 Å / Mean I/σ(I) obs: 2.57 / Num. unique obs: 5877 / CC_1/2: 0.747

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
HKL-3000		data reduction
HKL-3000		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.87→41.47 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2272	3803	3.3 %
R_work	0.192	-	-
obs	0.1931	60539	99.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.87→41.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5585	0	7	469	6061

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5723
X-RAY DIFFRACTION	f_angle_d	1.07	7768
X-RAY DIFFRACTION	f_dihedral_angle_d	11.199	841
X-RAY DIFFRACTION	f_chiral_restr	0.063	822
X-RAY DIFFRACTION	f_plane_restr	0.007	1035

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 (%)
1.87-1.89	0.3978	132	0.2953	3896	X-RAY DIFFRACTION	95
1.89-1.92	0.3028	144	0.2614	4152	X-RAY DIFFRACTION	99
1.92-1.95	0.2697	139	0.2486	4101	X-RAY DIFFRACTION	100
1.95-1.97	0.2793	143	0.2261	4117	X-RAY DIFFRACTION	100
1.97-2	0.2537	143	0.2245	4104	X-RAY DIFFRACTION	100
2-2.03	0.257	139	0.22	4149	X-RAY DIFFRACTION	100
2.03-2.07	0.2232	140	0.2104	4161	X-RAY DIFFRACTION	100
2.07-2.1	0.2626	143	0.2076	4107	X-RAY DIFFRACTION	100
2.1-2.14	0.2403	140	0.1992	4147	X-RAY DIFFRACTION	100
2.14-2.18	0.2335	140	0.1932	4158	X-RAY DIFFRACTION	100
2.18-2.23	0.2522	138	0.2	4101	X-RAY DIFFRACTION	100
2.23-2.28	0.2247	142	0.1942	4095	X-RAY DIFFRACTION	100
2.28-2.33	0.2708	137	0.1974	4140	X-RAY DIFFRACTION	100
2.33-2.39	0.2238	141	0.1959	4156	X-RAY DIFFRACTION	100
2.39-2.45	0.2697	141	0.1981	4119	X-RAY DIFFRACTION	100
2.45-2.52	0.279	148	0.1943	4188	X-RAY DIFFRACTION	100
2.52-2.61	0.2241	141	0.1995	4089	X-RAY DIFFRACTION	100
2.61-2.7	0.2418	135	0.1996	4124	X-RAY DIFFRACTION	100
2.7-2.81	0.2358	141	0.1966	4141	X-RAY DIFFRACTION	100
2.81-2.93	0.2629	138	0.1938	4124	X-RAY DIFFRACTION	100
2.93-3.09	0.2611	144	0.1952	4145	X-RAY DIFFRACTION	100
3.09-3.28	0.218	142	0.1878	4133	X-RAY DIFFRACTION	100
3.28-3.54	0.1913	143	0.1657	4146	X-RAY DIFFRACTION	100
3.54-3.89	0.155	143	0.154	4148	X-RAY DIFFRACTION	100
3.89-4.45	0.1755	146	0.1563	4130	X-RAY DIFFRACTION	100
4.46-5.61	0.1744	142	0.1689	4137	X-RAY DIFFRACTION	100
5.61-41.47	0.2608	138	0.2184	4128	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	3.6594	-1.1937	-1.0592	2.8549	0.0986	2.0987	-0.125	0.6058	-0.4109	-0.5928	-0.1043	0.603	0.1885	-0.4366	0.0839	0.2058	0.0105	-0.0763	0.2497	-0.0509	0.2107	48.1161	13.7752	29.1428
2	2.6901	0.3951	-0.6134	1.6969	-0.2427	1.5946	0.0053	-0.0962	0.089	0.1058	0.0237	0.0362	0.0286	-0.0522	-0.0145	0.114	-0.0056	0.0011	0.0941	0.0135	0.1031	57.5725	21.2425	38.7229
3	2.3262	-0.5444	-0.829	1.4855	0.2274	1.186	0.0828	-0.0475	0.2742	0.0353	0.0218	-0.1858	-0.2007	0.313	-0.0884	0.1833	-0.036	0.0226	0.1749	0.005	0.1955	76.7111	31.7709	33.5051
4	1.6973	0.8535	0.1082	1.554	-0.6091	1.1894	-0.0358	0.2121	-0.1561	-0.153	0.0175	-0.2607	0.1402	0.183	-0.0394	0.1775	0.0203	0.0433	0.1599	-0.0173	0.1585	64.1748	16.1637	32.6747
5	6.6843	-2.9452	2.278	3.3823	-1.2735	3.3699	0.1114	-0.3316	-0.1824	0.0005	-0.1805	0.3177	0.213	-0.1764	-0.0086	0.1693	-0.0406	0.0278	0.1845	0.0255	0.1434	48.444	12.6145	46.4325
6	3.534	-1.073	-0.7843	1.2126	0.7527	2.0575	-0.1426	0.1367	-0.497	0.068	-0.0217	0.0055	0.2553	-0.1886	0.1257	0.1819	-0.0296	0.0251	0.0963	-0.013	0.2406	53.3937	7.4707	37.1462
7	2.3768	-0.5091	-0.6134	1.1841	-0.2924	1	-0.2214	-0.1978	-0.1382	0.3048	0.2604	-0.3154	-0.2244	0.4314	-0.0382	0.1603	-0.0428	-0.0666	0.2687	-0.1046	0.2305	58.8218	35.4695	13.7578
8	1.4509	-0.0927	0.1378	2.2112	0.2158	1.1743	-0.0038	0.1073	-0.0045	-0.1398	0.0202	-0.3159	0.1029	0.23	-0.0178	0.1146	0.0097	-0.0038	0.1335	0.0021	0.1195	53.8353	29.2514	0.065
9	1.0332	-0.4071	0.1334	1.8111	-0.2914	0.8826	0.0459	0.0911	-0.066	-0.1878	0.0021	0.1157	0.1572	-0.0939	-0.0553	0.1423	0.0005	0.0041	0.1228	-0.015	0.1205	43.4679	30.9848	1.3024
10	6.5876	0.5962	-0.5896	1.5063	-0.6139	1.2687	-0.0411	0.679	-0.9323	-0.7603	-0.3588	1.1322	0.497	-0.4868	-0.0212	0.156	-0.0666	-0.1283	0.197	-0.0885	0.5323	28.2234	35.8797	-4.8971
11	1.9632	-0.3748	-0.167	0.9609	-0.4152	1.3607	-0.0763	0.1138	0.4257	-0.0692	-0.0234	0.4446	-0.2565	-0.3329	0.1534	0.1899	0.0491	-0.0187	0.2133	0.0058	0.3473	29.8651	42.0857	-2.0839
12	0.9167	-0.8262	0.3133	1.3784	-0.3756	1.2751	0.0533	-0.0888	-0.0393	0.0365	0.0269	0.2677	-0.0117	-0.0741	-0.0784	0.1503	-0.0064	0.0148	0.1421	-0.0162	0.1685	43.2917	30.4507	9.8667
13	7.0829	3.9656	-2.3379	4.1405	-1.5245	1.8176	0.4046	-0.5071	-0.248	0.2511	-0.3399	-0.2886	-0.0223	0.415	-0.0905	0.1991	0.0025	-0.0596	0.2119	-0.0113	0.2046	58.9249	18.9113	9.239
14	3.2296	-0.9827	-0.4143	1.5253	0.366	1.7151	-0.3977	-0.4735	-0.0957	0.2824	0.3175	-0.1873	0.1807	0.1721	0.0528	0.2003	0.043	-0.0369	0.193	0.0015	0.1394	53.1332	25.6468	16.7084
15	1.9355	-0.1334	1.2582	2.6448	-0.4048	1.1275	0.0853	0.8323	0.0645	-0.2645	-0.2143	-0.6984	-0.1531	0.3203	0.0612	0.2243	-0.0354	0.0873	0.4205	0.0422	0.245	37.4557	70.935	9.0759
16	2.775	0.6679	0.5679	2.0505	0.2695	1.8865	-0.003	0.0854	-0.3652	0.0745	0.1007	-0.2355	0.0394	0.2308	-0.0677	0.1244	0.005	0.0084	0.1551	-0.0294	0.143	29.118	62.3265	18.7807
17	1.9108	0.389	0.3278	1.2755	-0.2827	2.0241	-0.0254	0.0205	-0.449	-0.0306	0.1425	0.0367	0.4945	-0.6759	-0.0913	0.333	-0.1058	-0.0334	0.3704	-0.0457	0.2638	10.3884	52.2069	13.669
18	4.6311	-1.7965	-0.4071	2.8129	-0.3653	0.165	-0.2375	0.194	-0.3808	0.0494	0.1212	0.1921	-0.4641	-0.1622	0.0823	0.3479	-0.0374	-0.0716	0.3413	-0.0169	0.1767	16.1223	68.2026	4.6029
19	1.6024	0.5605	1.0356	1.304	-0.2204	1.8606	-0.0141	0.1322	-0.0425	-0.1035	0.0615	0.0797	-0.1495	0.0219	-0.0454	0.159	-0.0214	-0.0045	0.1574	0.007	0.1555	25.7577	67.7852	17.1969
20	6.5663	-3.1362	-1.7038	3.5715	1.4944	2.6186	0.1079	0.0592	0.3482	0.0773	0.0338	-0.5931	0.0065	0.3557	-0.1308	0.1931	-0.0313	-0.0319	0.2262	-0.0084	0.2015	38.1287	70.8871	26.7475
21	2.6847	-0.5054	0.8397	1.7575	-0.2864	1.69	-0.0459	0.132	0.2734	-0.1051	0.0768	-0.1639	-0.2915	0.2908	-0.0441	0.2213	-0.0851	-0.0039	0.2375	0.0276	0.1529	32.882	75.9431	17.1799

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 38 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 131 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 132 through 198 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 199 through 239 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 240 through 256 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 257 through 276 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 37 through 57 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 58 through 101 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 102 through 151 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 152 through 166 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 167 through 205 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 206 through 239 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 240 through 256 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 257 through 276 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 39 through 58 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 59 through 131 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 132 through 198 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 199 through 212 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 213 through 239 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 240 through 256 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 257 through 274 )

-
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://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