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

ID or keywords:

Entry

Database: PDB / ID: 4dtl

Title

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with ATP and Mn++

Components

VgrG protein

Keywords

TOXIN /

alpha-beta protein / G-actin cross linking toxin domain / 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: 2.39 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 of a VgrG Vibrio cholerae toxin ACD domain in complex with ATP and Mn++
Authors: Durand, E. / Audoly, G. / Derrez, E. / Spinelli, S. / Ortiz-Lombardia, M. / Cascales, E. / Raoult, D. / Cambillau, C.

History

Deposition	Feb 21, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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	4dtl.cif.gz	165.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4dtl.ent.gz	129.4 KB	Display	PDB format
PDBx/mmJSON format	4dtl.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	4dtd 4dtf 4dth 4dtq PDB Unreleased entry
Similar structure data	4dtd-d 4e1f-d 4e1c-d 4gqk-d 4dtf-d 6kz0-4 4dth-d 2yvu-d 6kz0-1 5bo4-5 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)	128.480, 128.480, 76.190
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: 43685.164 Da / Num. of mol.: 1 / Fragment: unp residues 717-1111 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: VC_1416, VgrG1 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KS45, UniProt: A0A0H3AIG7*PLUS

#1: Protein

VgrG protein

Mass: 43685.164 Da / Num. of mol.: 1 / Fragment: unp residues 717-1111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae (bacteria) / Strain: O395 / Gene: VC_1416, VgrG1 / Plasmid: pETG20A / Production host:

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

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Non-polymers , 5 types, 398 molecules

#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, 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-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.6 Å³/Da / Density % sol: 65.82 %
Crystal grow	Temperature: 293 K / pH: 6.3 Details: mixing 300 nL of protein at 13mg/mL with 100 nL of 2.4 M AmSO4, 0.1 M Bi-Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.3

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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: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.39→50 Å / Num. obs: 25641 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / B_iso Wilson estimate: 39.32 Å² / R_merge(I) obs: 0.129 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.39→2.46 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
BUSTER	2.11.2	refinement
XDS		data reduction
SCALA		data scaling
BUSTER	2.11.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.39→45.88 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.921 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.209	1307	5.1 %	RANDOM
R_work	0.191	-	-	-
obs	0.192	25603	99.1 %	-
all	-	25641	-	-

Displacement parameters

B_iso mean: 33.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.4848 Å²	0 Å²	0 Å²
2-	-	-2.4848 Å²	0 Å²
3-	-	-	4.9695 Å²

Refine analyze

Luzzati coordinate error obs: 0.29 Å

Refinement step

Cycle: LAST / Resolution: 2.39→45.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2757	0	54	391	3202

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	2918	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.08	3979	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1003	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		437	HARMONIC	5
X-RAY DIFFRACTION	t_it		2918	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	2.83
X-RAY DIFFRACTION	t_other_torsion	19.46
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion	0	389	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	3559	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.39→2.49 Å / Total num. of bins used: 13

	R_factor	Num. reflection	% reflection
R_free	0.246	144	5.38 %
R_work	0.2278	2531	-
all	0.2288	2675	-
obs	-	-	99.09 %

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	0.304	0.1707	0.0981	0.1799	-0.3174	0.002	0.0007	-0.0011	-0.0028	0.0015	-0.0002	-0.0067	0.0003	-0.0007	-0.0005	-0.0131	0.0018	0.0243	0.0153	0.007	-0.001	34.418	89.2306	16.5151
2	1.3301	0.2213	-0.2802	0	0.2942	0.003	0.0006	0.014	-0.0116	0.0075	0.0044	0.0094	0.0027	-0.0062	-0.0049	-0.045	-0.0194	-0.0118	0.0283	-0.0392	0.0068	46.1446	89.979	6.2411
3	0.3053	0.1357	0.2608	0.0011	0.3413	0.3206	0.0005	0.0145	-0.0121	-0.0104	-0.0017	-0.0008	0.007	0.0049	0.0012	-0.0489	0.0271	-0.0093	0.0489	-0.0325	0.002	55.3143	87.98	-7.2317
4	0.6014	0.2417	1.1617	0.0653	0.4665	0.8359	0.0011	0.0029	0.0062	0.0089	-0.0087	0	-0.0025	-0.0007	0.0076	-0.052	-0.0204	-0.0018	0.0415	-0.0307	-0.0233	46.5221	98.5589	11.2869
5	0.8036	-0.1641	0.0317	0	0.1145	0.0674	0.0016	-0.0063	-0.0002	0.0014	-0.0041	-0.0072	0.0031	0.006	0.0026	-0.0183	-0.0095	-0.0084	0.0344	-0.0227	-0.0191	54.1966	93.2212	9.4856
6	0.4475	0.5648	1.4974	0.1513	-0.8041	0.8888	0.0023	0.0004	0.0159	-0.0161	-0.0098	0	-0.0101	-0.0104	0.0075	-0.0317	-0.0056	0.0076	0.0196	0.0138	-0.0191	40.7968	99.1036	2.8129
7	0.6767	-0.4165	0.152	0	0.326	0.2983	0.0022	-0.0097	0.0056	0.0001	0.0055	0.0038	-0.003	-0.0163	-0.0077	-0.0785	0.0488	0.0078	0.0815	-0.0229	-0.0073	9.3035	91.3397	13.1242
8	1.3949	-0.7878	0.8557	0	-0.704	0.0293	0.0062	-0.0123	0.0089	-0.0057	-0.0118	0.0017	0.0065	-0.0081	0.0055	-0.0842	0.0297	-0.0253	0.0714	0.0111	-0.0121	12.4541	85.6717	3.9538
9	0.7104	-0.1626	-0.5715	0	0.0891	0.1369	-0.0009	0.0052	-0.0052	-0.0142	-0.0058	-0.0016	0.0037	0.0093	0.0067	-0.0233	0.0281	-0.0032	0.0403	0.0228	-0.024	20.6489	85.8837	-7.1138
10	1.3074	0.1394	-0.3574	0	-0.7257	0.7999	0.0037	0.005	-0.0244	0.0086	-0.0101	0.0007	0.0253	-0.0144	0.0064	-0.0948	-0.017	-0.0296	0.0883	0.0426	-0.0021	12.0087	78.3229	4.6773
11	0.8102	0.0578	0.3204	0.0009	-0.0053	0.0369	0.0028	-0.0047	0.0041	0.0068	-0.0064	-0.0011	-0.0009	-0.0078	0.0036	-0.0269	0.0042	-0.0185	0.0355	0.0459	-0.0206	26.1937	86.7265	15.7447
12	0.0186	-0.0983	-0.0019	0.1623	0.0072	0.025	0.0001	-0.0002	0.0028	-0.0034	0.0003	-0.0005	-0.0067	0.0009	-0.0004	-0.0071	0.0084	0.0125	0.0025	0.0027	0.0116	32.6433	105.04	10.4766
13	0.0087	0.0952	0.0164	0	0.0176	0.0046	0	-0.0009	-0.0008	-0.0027	0.0004	-0.0001	0.0007	-0.0002	-0.0005	-0.0083	-0.0164	-0.0129	0.0066	-0.0048	-0.0024	33.3846	89.0463	9.4254

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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