PDB-4e1d: Structure of a VgrG Vibrio cholerae toxin ACD domain in complex w...

ID or keywords:

Entry

Database: PDB / ID: 4e1d

Title

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

Components

VgrG protein

Keywords

TOXIN / alpha beta protein / G-actin cross-linking toxin / G-actin (substrate)

Function / homology

Function and homology information

isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine / isopeptide cross-linking / acid-amino acid ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / actin filament depolymerization / host cell cytosol / toxin activity / host cell cytoplasm / magnesium ion binding / extracellular region / ATP binding
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.49 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 / pdbx_struct_conn_angle / struct_conn / 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_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_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.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_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	4e1d.cif.gz	155.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4e1d.ent.gz	120.9 KB	Display	PDB format
PDBx/mmJSON format	4e1d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4e1d_validation.pdf.gz	749.1 KB	Display	wwPDB validaton report
Full document	4e1d_full_validation.pdf.gz	749.5 KB	Display
Data in XML	4e1d_validation.xml.gz	9.2 KB	Display
Data in CIF	4e1d_validation.cif.gz	13.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e1/4e1d ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1d	HTTPS FTP

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Related structure data

Related structure data	4e1cSC 4e1fC 4dtd 4dtf 4dth 4dtl S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4dtf-d 4e1c-d 4dth-d 4gqk-d 4dtd-d 4pi3-d 4e1f-d 2oz2-d 5bmu-4 5bmu-3 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

44.6 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)	128.390, 128.390, 76.720
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

#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
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.62 Å³/Da / Density % sol: 66.01 %

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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 4, 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: 2.49→50 Å / Num. obs: 42340 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / B_iso Wilson estimate: 43.43 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 10.2
Reflection shell	Resolution: 2.49→2.56 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.416 / Mean I/σ(I) obs: 3 / % possible all: 94.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E1C

4e1c

Resolution: 2.49→45.39 Å / Cor.coef. F_o:F_c: 0.825 / Cor.coef. F_o:F_c free: 0.801 / SU R Cruickshank DPI: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.241	951	4.18 %	RANDOM
R_work	0.222	-	-	-
obs	0.223	22761	98.8 %	-
all	-	22761	-	-

Displacement parameters

B_iso mean: 30.88 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.4987 Å²	0 Å²	0 Å²
2-	-	-5.4987 Å²	0 Å²
3-	-	-	10.9974 Å²

Refine analyze

Luzzati coordinate error obs: 0.36 Å

Refinement step

Cycle: LAST / Resolution: 2.49→45.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2757	0	44	136	2937

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	2885	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.06	3927	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		990	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		2885	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	2.47
X-RAY DIFFRACTION	t_other_torsion	19.44
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	3326	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.49→2.61 Å / Total num. of bins used: 11

	R_factor	Num. reflection	% reflection
R_free	0.2615	121	4.14 %
R_work	0.2304	2799	-
all	0.2317	2920	-
obs	-	-	98.81 %

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	0.2548	0.2312	0.16	0.2619	-0.2428	0.1581	0.0007	-0.0017	-0.0026	0.008	0.0019	-0.0039	0.0024	-0.0066	-0.0026	0.0061	0.0048	0.0014	0.0171	0.0204	0.0137	34.4052	89.1664	16.5802
2	0.5591	-0.1479	-0.274	0	0.2767	0	0	-0.0094	0.0006	0.0158	0.0043	0.0009	-0.0017	-0.0048	-0.0043	-0.0518	-0.0164	-0.009	0.0135	0.0197	0.0272	46.0951	89.9733	6.279
3	0.0344	0.0439	-0.1146	0.1186	-0.0197	0	-0.0002	0.006	-0.0066	-0.0023	0.005	-0.0003	-0.0024	0.0068	-0.0048	-0.0317	-0.0199	0.0092	-0.0088	-0.0081	0.018	55.2347	88.0492	-7.2223
4	0.001	-0.2173	0.2039	0.0033	-0.1842	0.0073	0.0012	-0.0215	0.0081	0.0152	-0.0015	-0.0074	-0.0049	-0.0263	0.0002	-0.0398	-0.0021	-0.0105	0.0088	0.0117	0.0019	46.4972	98.5248	11.3811
5	0.1414	-0.3474	-0.1336	0	0.029	0.0004	0.0005	-0.013	-0.0039	0.0134	-0.0011	-0.002	-0.0017	0.002	0.0006	-0.0246	-0.0001	-0.0017	0.0143	-0.0065	0.0044	54.1639	93.1939	9.5281
6	0.1848	-0.1632	0.4357	0.009	-0.4619	0.1118	0.0008	-0.0105	-0.0024	-0.0051	0.0035	-0.0124	-0.0032	-0.0158	-0.0044	-0.0259	-0.0121	0.0119	-0.0097	0.0253	0.0105	40.7538	99.1257	2.9213
7	0.3729	-0.1454	-0.1217	0	0.0427	0.1947	0.0012	-0.0082	0.0002	0.0051	0	0.0038	-0.0072	-0.0039	-0.0012	-0.0647	0.01	0.0036	0.0512	0.0051	0.0055	9.2846	91.3206	13.2702
8	0.3834	-0.9379	0.1333	0	-0.3339	0.0004	0.0038	-0.0249	0.0035	0.0211	-0.0081	-0.0065	-0.0013	-0.0103	0.0043	-0.0801	0.0139	-0.0083	0.0222	0.0128	0.014	12.4122	85.7006	4.0558
9	0.511	-0.0446	-0.2718	0	0.1387	0.0009	-0.0003	-0.007	0.0039	-0.0012	-0.0023	-0.005	0.0076	0.0032	0.0026	-0.0439	0.0069	-0.0071	0.0023	0.0036	0.014	20.5665	85.9637	-7.0358
10	0.9032	0.0577	-0.2551	0	-1.3437	0.3228	0.0022	-0.0034	-0.0116	0.0344	-0.0079	-0.0019	0.0151	-0.0106	0.0057	-0.081	-0.0482	-0.0172	0.0471	0.0432	0.0159	11.9668	78.3427	4.7469
11	0.4644	0.1431	0.095	0	-0.2806	0	0.0008	-0.0158	0.0026	0.0222	-0.0001	0.0028	0.0063	-0.0063	-0.0007	-0.0217	-0.0185	-0.0079	0.021	0.0296	0.0064	26.177	86.6694	15.8146
12	0.0405	-0.0868	0.019	0.1189	-0.0005	0	-0.0002	-0.0028	0.0002	0.0015	0.0005	0.002	-0.002	-0.002	-0.0002	-0.0111	-0.0005	0.0053	0.0009	-0.0014	0.0085	32.6212	105.0237	10.6475
13	0.0786	0.0036	0.0458	0.0947	-0.0318	0.0212	-0.0005	0.0012	-0.0023	-0.0014	0.0011	0.0007	0.0008	0.0004	-0.0006	0.0195	-0.0006	-0.0018	0.0225	0.0051	0.016	33.567	88.7836	10.1476

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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