PDB-5xn7: Crystal structure of the effector domain RID of Vibrio vulnificus...

ID or keywords:

Entry

Database: PDB / ID: 5xn7

Title

Crystal structure of the effector domain RID of Vibrio vulnificus MARTX toxin

Components

Putative RTX-toxin

Keywords

TOXIN

Function / homology

Function and homology information

host cell cytosol / peptidase activity / transferase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / membrane
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.7 Å

Authors

Yin, L. / Zhu, Y.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of a MARTX toxin effector domain
Authors: Yin, L. / Zhu, Y.

History

Deposition	May 18, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 27, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5xn7.cif.gz	436.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5xn7.ent.gz	355.9 KB	Display	PDB format
PDBx/mmJSON format	5xn7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5xn7_validation.pdf.gz	490.8 KB	Display	wwPDB validaton report
Full document	5xn7_full_validation.pdf.gz	513.5 KB	Display
Data in XML	5xn7_validation.xml.gz	41.2 KB	Display
Data in CIF	5xn7_validation.cif.gz	56.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xn/5xn7 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/5xn7	HTTPS FTP

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Related structure data

Similar structure data	5irc-d 6e53-d 3kyl-d 5xp8-d 4het-d 5mbj-d 3pvt-d 1w7t-d 5jk6-d 5wwr-1 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	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Putative RTX-toxin

B: Putative RTX-toxin

hetero molecules

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

1

A: Putative RTX-toxin

hetero molecules

defined by author&software
Evidence: gel filtration
69.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative RTX-toxin

hetero molecules

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

Unit cell

Length a, b, c (Å)	124.743, 185.185, 81.365
Angle α, β, γ (deg.)	90.00, 95.60, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 2 molecules AB

#1: Protein	Putative RTX-toxin Mass: 68578.477 Da / Num. of mol.: 2 / Fragment: effector domain, UNP residues 380-995 / Mutation: C2835A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: rtxA1 / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F1CLG1

#1: Protein

Putative RTX-toxin

Mass: 68578.477 Da / Num. of mol.: 2 / Fragment: effector domain, UNP residues 380-995 / Mutation: C2835A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio vulnificus (bacteria) / Gene: rtxA1 / Plasmid: pET28a-SUMO / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F1CLG1

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Non-polymers , 6 types, 98 molecules

#2: Chemical	ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₈O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.43 Å³/Da / Density % sol: 64.11 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 6% 1,4 Dioxane, 0.1M MES pH6.5, 1.6M (NH4)2SO4

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Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.97776 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.97776 Å / Relative weight: 1

Reflection

Resolution: 2.69→103.12 Å / Num. obs: 50131 / % possible obs: 99.9 % / Redundancy: 6.8 % / R_merge(I) obs: 0.127 / R_pim(I) all: 0.052 / R_rim(I) all: 0.137 / Χ²: 0.718 / Net I/σ(I): 3.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.7-2.75	6	0.759	0.85	0.328	0.828	0.42	98.9
2.75-2.8	5.9	0.705	0.879	0.312	0.773	0.43	100
2.8-2.85	6.3	0.596	0.921	0.257	0.65	0.441	100
2.85-2.91	6.8	0.508	0.937	0.209	0.55	0.445	100
2.91-2.97	7.1	0.43	0.966	0.173	0.464	0.455	100
2.97-3.04	7.1	0.392	0.966	0.158	0.423	0.477	100
3.04-3.12	7.1	0.359	0.969	0.145	0.388	0.483	100
3.12-3.2	7.1	0.276	0.978	0.111	0.298	0.506	100
3.2-3.3	7	0.225	0.985	0.091	0.243	0.543	100
3.3-3.4	7	0.181	0.986	0.073	0.195	0.591	100
3.4-3.52	6.8	0.159	0.989	0.066	0.172	0.594	100
3.52-3.66	6.3	0.138	0.989	0.06	0.151	0.675	100
3.66-3.83	6.8	0.122	0.992	0.051	0.133	0.734	100
3.83-4.03	7.3	0.111	0.993	0.044	0.119	0.772	100
4.03-4.29	7.2	0.1	0.994	0.04	0.107	0.9	100
4.29-4.62	7.1	0.093	0.993	0.038	0.101	0.971	100
4.62-5.08	6.9	0.09	0.992	0.037	0.098	1.037	100
5.08-5.81	6.4	0.092	0.991	0.04	0.1	0.973	100
5.81-7.32	7.3	0.09	0.993	0.036	0.097	1.023	100
7.32-50	6.7	0.074	0.994	0.031	0.08	1.78	99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
DENZO		data collection
SCALEPACK		data scaling
PDB_EXTRACT	3.22	data extraction
DENZO		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.7→50 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.923 / SU B: 24.165 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24378	2554	5.1 %	RANDOM
R_work	0.2033	-	-	-
obs	0.20536	47537	99.51 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 78.401 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.67 Å²	0 Å²	-0.51 Å²
2-	-	7.71 Å²	0 Å²
3-	-	-	-4.14 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8248	0	47	89	8384

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	8431
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.311	1.947	11420
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.79	5	1082
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.011	25.256	390
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.758	15	1287
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.751	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	1296
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6396
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.393	170	-
R_work	0.353	3273	-
obs	-	-	93.81 %

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	6.1215	-2.6923	-0.1918	5.1602	-1.9713	1.0805	0.3741	0.177	-0.0641	0.2881	0.0273	0.9131	-0.318	-0.1126	-0.4014	1.3317	0.0714	-0.1136	0.6501	0.2024	1.1752	44.0843	60.539	15.25
2	3.9553	1.5568	-2.1217	6.6557	-2.2745	5.0092	-0.0142	0.1173	0.8282	-0.3579	-0.0132	-0.071	-0.9188	0.3578	0.0274	0.4374	-0.0822	-0.0404	0.0645	0.0654	0.3118	51.8317	37.8879	27.5211
3	5.5279	0.5877	-0.1273	0.8748	-0.2013	2.0419	-0.1312	0.6105	0.1809	0.0301	0.0431	0.0308	-0.1306	0.2384	0.0881	0.1813	0.0028	-0.011	0.1809	0.0157	0.0138	60.4436	23.2137	14.5067
4	4.7555	-0.4077	-2.8274	2.8895	2.5536	4.776	0.6862	0.3964	1.3008	-0.1722	-0.1304	-0.4834	-1.497	0.1821	-0.5558	1.018	-0.1862	-0.153	0.7915	0.1676	0.8584	85.8293	43.4359	32.0892
5	5.3862	0.5494	1.7645	2.3894	-0.2083	3.8608	0.0395	0.2922	-0.3338	0.0409	-0.003	-0.1424	0.1525	0.3393	-0.0365	0.1155	-0.0269	-0.0041	0.3634	0.0256	0.0641	78.2196	19.5568	18.7704
6	3.4328	0.436	-0.1262	7.9901	3.3879	4.0727	-0.0974	0.3026	-0.6369	-0.6228	0.2716	0.0416	0.7202	-0.3862	-0.1742	0.838	-0.0954	-0.1204	0.8791	-0.2283	0.7301	16.8922	-8.6721	0.0199
7	7.0369	-0.7398	-0.0231	3.5131	-0.7322	4.0798	0.1168	0.5278	0.0818	-0.0833	-0.0304	0.1097	0.1132	0.0123	-0.0865	0.1579	0.0064	-0.0009	0.3798	-0.0276	0.1529	21.702	15.906	12.5939
8	7.1973	2.8381	-1.1268	3.4449	-1.0346	4.9616	-0.0039	0.6327	0.435	-0.4258	0.0508	-0.0663	-0.2387	-0.505	-0.047	0.1973	0.0802	-0.0157	0.525	0.0196	0.1925	1.1652	22.9458	18.5904
9	6.5755	-1.2488	-0.4689	2.5002	0.1675	3.086	0.0559	-0.3488	-1.2524	-0.0618	0.0184	-0.0605	0.7749	-0.0387	-0.0742	0.3771	-0.0894	-0.0047	0.2779	0.0698	0.4167	23.0632	0.5143	40.5903
10	4.2038	-0.088	0.7347	2.0693	-0.3731	3.2446	-0.11	-0.3583	-0.0233	0.0629	0.0625	-0.1151	0.0485	-0.3062	0.0475	0.1255	-0.0335	-0.0078	0.16	0.023	0.1184	22.2053	13.1304	42.3531

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2284 - 2374
2	X-RAY DIFFRACTION	2	A	2375 - 2474
3	X-RAY DIFFRACTION	3	A	2475 - 2654
4	X-RAY DIFFRACTION	4	A	2655 - 2773
5	X-RAY DIFFRACTION	5	A	2774 - 2886
6	X-RAY DIFFRACTION	6	B	2284 - 2373
7	X-RAY DIFFRACTION	7	B	2374 - 2466
8	X-RAY DIFFRACTION	8	B	2467 - 2574
9	X-RAY DIFFRACTION	9	B	2575 - 2745
10	X-RAY DIFFRACTION	10	B	2746 - 2881

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