5XN7: Putative RTX-toxin

Name: PDB 5XN7: Crystal structure of the effector domain RID of Vibrio vulnificus MARTX toxin
Published: 2017-09-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of the effector domain RID of Vibrio vulnificus MARTX toxin. Determined by X-ray diffraction at 2.7 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Vibrio vulnificus
Chains: 2
Atoms: 8,384
Mol. weight: 137.97 kDa
Ligands: DIO
Released: 27 Sept 2017

Explore 5XN7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XN7 contains 71 α-helices and 31 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 34 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2286-2288	3	1
β-strand	2294-2297	4	1
β-strand	2309-2311	3	1
β-strand	2312	1	2
α-helix	2324-2330	7
β-strand	2340-2343	4	2
β-strand	2347-2352	6	2
β-strand	2355-2361	7	2
α-helix	2374-2377	4
α-helix	2378-2384	7
α-helix	2394-2409	16
α-helix	2419-2437	19
α-helix	2444-2462	19
α-helix	2477-2481	5
α-helix	2484-2487	4
α-helix	2493	1
β-strand	2494	1	3
α-helix	2495	1
β-strand	2496-2497	2	4
β-strand	2503-2504	2	4
α-helix	2510-2515	6
α-helix	2522-2545	24
α-helix	2549-2552	4
β-strand	2560	1	3
α-helix	2561-2575	15
β-strand	2580-2587	8	5
α-helix	2592-2594	3
β-strand	2595-2600	6	5
α-helix	2610-2618	9
β-strand	2620-2621	2	5
α-helix	2626-2635	10
α-helix	2651-2654	4
α-helix	2680-2692	13
α-helix	2707-2715	9
α-helix	2717-2720	4
α-helix	2721-2723	3
α-helix	2727-2739	13
α-helix	2744-2761	18
α-helix	2765-2773	9
α-helix	2774-2778	5
α-helix	2779-2794	16
β-strand	2798-2805	8	5
α-helix	2810-2819	10
α-helix	2824-2831	8
α-helix	2835-2845	11
α-helix	2848-2852	5
α-helix	2855-2856	2
α-helix	2859-2861	3
α-helix	2865-2883	19

Chain B: 37 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2285-2287	3	6
β-strand	2295	1	7
β-strand	2296-2298	3	6
β-strand	2310-2312	3	7
α-helix	2319-2330	12
α-helix	2334-2336	3
β-strand	2340-2342	3	7
β-strand	2347-2352	6	7
β-strand	2355-2361	7	7
β-strand	2368-2369	2	7
α-helix	2370-2372	3
α-helix	2378-2384	7
α-helix	2390-2393	4
α-helix	2394-2412	19
α-helix	2418-2437	20
α-helix	2444-2462	19
α-helix	2478-2481	4
α-helix	2493	1
β-strand	2494	1	8
α-helix	2495	1
β-strand	2496-2497	2	9
β-strand	2503-2504	2	9
α-helix	2522-2535	14
α-helix	2537-2545	9
α-helix	2549-2552	4
β-strand	2560	1	8
α-helix	2561-2575	15
β-strand	2580-2587	8	10
β-strand	2595-2600	6	10
α-helix	2601	1
α-helix	2610-2618	9
β-strand	2620-2621	2	10
α-helix	2626-2635	10
α-helix	2644-2646	3
α-helix	2651-2653	3
α-helix	2679-2694	16
α-helix	2702-2705	4
α-helix	2706-2715	10
α-helix	2717-2720	4
α-helix	2727-2730	4
α-helix	2731-2737	7
α-helix	2743-2747	5
α-helix	2748-2761	14
α-helix	2765-2773	9
α-helix	2774-2778	5
α-helix	2779-2794	16
β-strand	2798-2805	8	10
α-helix	2810-2820	11
α-helix	2824-2831	8
α-helix	2835-2845	11
α-helix	2848-2852	5
α-helix	2859-2861	3
α-helix	2865-2879	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putative RTX-toxin	A, B	protein	616	Vibrio vulnificus	A0A2S3R7M0

Sequence of entity 1 (A, B), FASTA

>5XN7_1 Putative RTX-toxin (chains A, B)
RNLLVQEGEEGFEVRSWPGTDGKSKTILLDNPEDAAQQKSIERFILANFDNFEQMPDELF
LVDNKVLSHHDGRTRILARKEDGAWTYNANVELMSVTELLDAAHVSGKVRGESYQQVIDA
LTEYHASTAEHADYELTSVEKLLNLRKQVEGYVLGHPDSGRVQAMNALLNQVNSRLEAVS
VLVVSEQSIKAHDSFSHLYDQLDNANLKESKHLYLDGNGDFVTKGKGNLANIDKLGGSDA
VLEKVKAAVSHEYGQVVADTIFAGLSANDLAKDGKGIDIAGLNKVHQAIEQHMSPVSATM
YIWKPSDHSALGHAALQIGQGRTQLEGQAAADFNKQNYVSWWPLGSKSSNIRNIFNVATE
DQPDLKLRWSDFSQPAHQNDTLEHDMASEENDGFGLNDGETKLKRFVEKLNAAKGIDASY
KDASEGYASVLLGNPDMLASTGIPAHVFQPFVDQWNDTSYDMMDVANRFAEELQKQAQAS
GDPALVEKRIDNVVRLFAERALEEIEAFKASQADEGRVFRINLEGLDVAAMQAEWNRLSN
DPDARYQLLTKNASSTVAKVLKAGGADKLIGHTWRPKFGVWTPTELFNFGQALQEAQLEI
AAKKQSHQATDLLDAL

Ligands and cofactors

ID	Name	Formula	Copies
DIO	1,4-diethylene dioxide	C4 H8 O2	2

Water and common crystallization additives (SO4, MES, CL, FMT) are not listed.

Primary citation

Crystal structure of a MARTX toxin effector domain. Yin, L., Zhu, Y. To be published.

Other PDB entries of the same protein (UniProt A0A2S3R7M0), best resolution first:

8YJC 1.3 Å, Structure of Vibrio vulnificus MARTX cysteine protease domain C3727A
8YJA 2.2 Å, Structure of Vibrio vulnificus MARTX cysteine protease domain lacking beta-flap
8KA0 2.35 Å, Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain…
8KA1 2.82 Å, Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain…
8K9Z 2.9 Å, Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain…
8KA2 3.38 Å, Crystal structure of the RID-dependent transforming NADase domain…
2N9W Solution NMR Structure of the membrane localization domain from the Ras/Rap1-specific…

Browse structure collections

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