PDB-4e1c: Structure of a VgrG Vibrio cholerae toxin ACD domain in complex w...

ID or keywords:

Entry

Database: PDB / ID: 4e1c

Title

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with ADP and Mg++

Components

VgrG protein

Keywords

TOXIN / Alpha Beta protein / G-actin cross-linking Toxin / G-actin

Function / homology

Function and homology information

isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine / isopeptide cross-linking /

Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / acid-amino acid ligase activity / actin filament depolymerization / host cell cytosol /

toxin activity / host cell cytoplasm / magnesium ion binding / extracellular region /

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Durand, E. / Audoly, G. / Derrez, E. / Spinelli, S. / Ortiz-Lombardia, M. / Cascales, E. / Raoult, D. / Cambillau, C.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structure and functional characterization of the Vibrio cholerae toxin from the VgrG/MARTX family.
Authors: Durand, E. / Audoly, G. / Derrez, E. / Spinelli, S. / Ortiz-Lombardia, M. / Cascales, E. / Raoult, D. / Cambillau, C.

History

Deposition	Mar 6, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4e1c.cif.gz	166.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4e1c.ent.gz	129.2 KB	Display	PDB format
PDBx/mmJSON format	4e1c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e1/4e1c ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1c	HTTPS FTP

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Related structure data

Related structure data	4e1dC 4e1fC 4dtfS 4dtd 4dth 4dtl S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4dtd-d 4gqk-d 4dtf-d 4e1f-d 4dtl-d 4e1d-d 4dth-d 6kz0-4 2yvu-d 6kz0-1 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: VgrG protein

hetero molecules

44.7 kDa, 1 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)	128.460, 128.460, 76.390
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

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Protein , 1 types, 1 molecules A

#1: Protein	VgrG protein Mass: 43742.215 Da / Num. of mol.: 1 / Fragment: Vibrio cholerae VgrG1 ACD (unp residues 716-1111) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: VC_1416, VgrG1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KS45, UniProt: A0A0H3AIG7*PLUS

#1: Protein

VgrG protein

Mass: 43742.215 Da / Num. of mol.: 1 / Fragment: Vibrio cholerae VgrG1 ACD (unp residues 716-1111)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae (bacteria) / Strain: O395 / Gene: VC_1416, VgrG1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KS45, UniProt: A0A0H3AIG7*PLUS

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Non-polymers , 5 types, 478 molecules

#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.61 Å³/Da / Density % sol: 65.9 %
Crystal grow	Temperature: 293 K / pH: 6.3 Details: 300 nL of protein at 13mg/mL, 100 nL of 2.4 M AmSO4, 0.1 M Bi-Tris, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 2012 / Details: MIRRORS
Radiation	Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.25→50 Å / Num. obs: 28824 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / B_iso Wilson estimate: 39.49 Å² / R_merge(I) obs: 0.053 / Net I/σ(I): 21.4
Reflection shell	Resolution: 2.25→2.3 Å / Redundancy: 4 % / R_merge(I) obs: 0.436 / Mean I/σ(I) obs: 3.7 / % possible all: 93.2

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
BUSTER	2.11.2	refinement
HKL-3000		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DTF

4dtf

Resolution: 2.25→40.62 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.933 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.196	1019	3.55 %	RANDOM
R_work	0.174	-	-	-
obs	0.175	28721	92.9 %	-
all	-	28721	-	-

Displacement parameters

B_iso mean: 37.25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.2882 Å²	0 Å²	0 Å²
2-	-	-2.2882 Å²	0 Å²
3-	-	-	4.5764 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: LAST / Resolution: 2.25→40.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2757	0	55	470	3282

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	2888	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.08	3932	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		989	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		80	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		422	HARMONIC	5
X-RAY DIFFRACTION	t_it		2888	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	3.23
X-RAY DIFFRACTION	t_other_torsion	19.17
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion	0	385	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	0	3579	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.25→2.33 Å / Total num. of bins used: 14

	R_factor	Num. reflection	% reflection
R_free	0.2235	107	3.5 %
R_work	0.208	2954	-
all	0.2085	3061	-
obs	-	-	92.92 %

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	0.1942	0.2158	0.0935	0.0971	-0.1793	0.0358	0.0018	-0.003	-0.0021	0.0031	-0.0002	-0.0034	0.003	-0.0032	-0.0016	-0.0186	-0.0137	0.0191	0.0267	0.0082	-0.0063	34.3198	89.1554	16.5402
2	1.4269	0.3882	-0.3824	0	0.1996	0.0053	0.0008	0.0047	-0.0176	0.0112	0.0021	0.0057	0.0014	-0.0097	-0.0028	-0.0421	-0.0256	-0.0098	0.0494	-0.0139	-0.0118	46.1439	90.0334	6.3373
3	0.3571	-0.016	0.3797	0	0.2034	0.6518	0.0007	0.0089	-0.011	-0.0076	0.0012	-0.0005	0.0081	-0.0018	-0.0019	-0.0418	0.0132	-0.0019	0.0527	-0.0312	-0.0091	55.2183	87.9177	-7.2292
4	0.545	0.069	0.888	0.0361	0.3473	0.6086	-0.0006	-0.011	0.0108	0.0145	-0.013	-0.0042	-0.0016	-0.014	0.0136	-0.055	-0.0236	-0.0165	0.0366	-0.0155	-0.011	46.4501	98.486	11.3262
5	0.9327	-0.1936	0.1953	0	0.2044	0.0006	0.0013	-0.0093	-0.0021	-0.001	-0.0054	-0.0038	0.0001	0.0074	0.0041	-0.031	-0.0004	-0.0077	0.0475	-0.0195	-0.0185	54.1067	93.1353	9.4907
6	0.1697	0.5307	0.7565	0.1468	-0.251	0.4696	-0.001	-0.001	0.0065	-0.0097	0.0022	-0.0041	-0.0225	-0.0002	-0.0013	-0.0353	0.0019	0.0151	0.014	0.0034	-0.0056	40.7054	99.0417	2.8214
7	0.6431	-0.3156	-0.096	0	0.5244	0.2282	0.0014	-0.0084	0.0021	0.0055	0.0073	0.0033	-0.0081	-0.0144	-0.0087	-0.0848	0.0476	-0.0062	0.0855	-0.0585	-0.0024	9.2252	91.2122	13.1717
8	1.1905	-0.1708	0.8192	0	-0.4167	0.0717	0.0043	-0.0303	-0.0015	-0.0067	-0.0071	0.0009	0.003	-0.012	0.0028	-0.0875	0.0254	-0.0394	0.0692	-0.0072	0.0032	12.4292	85.5843	3.9803
9	0.7822	0.0555	-0.6829	0	-0.1104	0.4858	-0.0062	0.0058	-0.0017	-0.0073	0.0035	-0.003	0.0075	0.0058	0.0027	-0.0394	-0.0037	-0.0282	0.0538	0.0126	-0.0203	20.6156	85.8448	-7.1369
10	1.3173	0.3516	-0.2332	0	-0.9208	0.7439	0.0016	-0.0085	-0.0225	0.0086	-0.011	0.003	0.0229	-0.0171	0.0094	-0.1163	-0.0269	-0.0416	0.0972	0.034	0.0085	12.0113	78.2483	4.6769
11	0.7227	0.5824	0.4544	0	-0.1907	0.0393	0.0008	-0.0071	-0.0028	0.0089	-0.0034	0.002	0.0023	-0.0074	0.0026	-0.0319	-0.0025	-0.027	0.045	0.0271	-0.0122	26.2265	86.4324	15.7443
12	0.0349	-0.0574	0.042	0.0784	0.0299	0.0359	0.0001	-0.0017	0.0023	-0.0029	-0.0012	-0.0003	-0.0053	-0.0017	0.0012	-0.0071	0.0094	0.0085	0.0104	-0.0099	0.0019	32.5336	105.009	10.5272
13	0.0334	0.0161	0.0189	0	0	0.0053	0.0006	-0.0002	-0.0007	-0.0022	-0.0002	0	0.0012	0.0003	-0.0003	-0.0062	-0.0085	-0.0024	0.0079	-0.0055	-0.0004	33.3948	88.5417	10.327

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|0 - A\|17 }
2	X-RAY DIFFRACTION	2	{ A\|18 - A\|53 }
3	X-RAY DIFFRACTION	3	{ A\|54 - A\|78 }
4	X-RAY DIFFRACTION	4	{ A\|79 - A\|116 }
5	X-RAY DIFFRACTION	5	{ A\|117 - A\|143 }
6	X-RAY DIFFRACTION	6	{ A\|144 - A\|170 }
7	X-RAY DIFFRACTION	7	{ A\|171 - A\|206 }
8	X-RAY DIFFRACTION	8	{ A\|207 - A\|236 }
9	X-RAY DIFFRACTION	9	{ A\|237 - A\|269 }
10	X-RAY DIFFRACTION	10	{ A\|270 - A\|319 }
11	X-RAY DIFFRACTION	11	{ A\|320 - A\|343 }
12	X-RAY DIFFRACTION	12	{ A\|344 - A\|355 }
13	X-RAY DIFFRACTION	13	{ A\|401 - A\|401 }

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