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- PDB-4e1f: Structure of a VgrG Vibrio cholerae toxin ACD domain Glu16Gln mut... -

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Basic information

Entry
Database: PDB / ID: 4e1f
TitleStructure of a VgrG Vibrio cholerae toxin ACD domain Glu16Gln mutant in complex with ADP and Mn++
ComponentsVgrG protein
KeywordsTOXIN / 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 / 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 / ATP binding
Similarity search - Function
Actin cross-linking domain / TerB-like / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail baseplate hub (GPD) / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain ...Actin cross-linking domain / TerB-like / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail baseplate hub (GPD) / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Actin cross-linking toxin VgrG1 / Actin cross-linking toxin VgrG1
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDurand, E. / Audoly, G. / Derrez, E. / Spinelli, S. / Ortiz-Lombardia, M. / Cascales, E. / Raoult, D. / Cambillau, C.
CitationJournal: 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
DepositionMar 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VgrG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,89610
Polymers43,7411
Non-polymers1,1559
Water8,503472
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VgrG protein
hetero molecules

A: VgrG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,79220
Polymers87,4822
Non-polymers2,30918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/41
Buried area6720 Å2
ΔGint-212 kcal/mol
Surface area30400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.130, 129.130, 77.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein VgrG protein


Mass: 43741.230 Da / Num. of mol.: 1 / Fragment: Vibrio cholerae VgrG1 ACD (unp residues 716-1111) / Mutation: E16Q
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 / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 23, 2012 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 72859 / Num. obs: 72859 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 27.45 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 0.363
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 10.1 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E1D

4e1d


Resolution: 2.1→46.22 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 1210 3.14 %RANDOM
Rwork0.173 ---
obs0.1735 38592 99.96 %-
all-38592 --
Displacement parametersBiso mean: 29.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.7917 Å20 Å20 Å2
2---2.7917 Å20 Å2
3---5.5835 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 63 472 3288
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012885HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13930HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d982SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes419HARMONIC5
X-RAY DIFFRACTIONt_it2885HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion19.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion0384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3554SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2264 93 3.15 %
Rwork0.1914 2858 -
all0.1925 2951 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.2710.11340.11330-0.272600.0019-0.0032-0.00720.00270.0016-0.01190.0058-0.0062-0.0035-0.0261-0.02130.02230.02910.0178-0.013834.53589.537116.5599
21.33180.4477-0.319400.19940.17490.0041-0.0104-0.0115-0.0049-0.00570.01030.006-0.00550.0015-0.0296-0.00990.01950.04660.0182-0.019546.386490.3376.336
30.39110.24220.17030.03290.34120.43850.0010.0085-0.0137-0.01290.008-0.00110.0089-0.0035-0.009-0.044-0.0060.00810.0451-0.02350.006155.50488.1814-7.2006
40.45290.17870.6030.1999-0.00120.70110.0004-0.02360.01140.0153-0.0141-0.00340.0042-0.02940.0136-0.0492-0.04030.01360.04260.0005-0.0246.705898.81811.3013
50.93220.1192-0.004400.28680.0537-0.0024-0.0229-0.0049-0.00630.0003-0.00370.00470.00660.0021-0.0281-0.00730.01040.05560.0072-0.021754.345693.43989.5016
60.08580.27250.45460.2234-0.21340.4737-0.0011-0.00990.0197-0.0161-0.00790.0024-0.0219-0.01240.009-0.0369-0.00840.0320.02280.0079-0.00440.981999.35342.8013
70.74410.0201-0.308600.07040.45530.002-0.00750.00760.00730.00910.005-0.0129-0.006-0.0111-0.10050.0310.02520.1227-0.021-0.02599.422291.707413.1352
81.25120.24720.65770.0493-0.28040.05190.0034-0.03280.0018-0.007-0.00450.00060.0014-0.01110.001-0.10330.0022-0.0110.08470.0068-0.00212.56885.97423.998
91.12890.0987-0.51290.019-0.25370.4781-0.0063-0.00370.0029-0.01580.0082-0.00420.0149-0.0028-0.002-0.04170.00130.00040.06550.0254-0.033520.832886.0856-7.0622
101.5086-0.1538-0.4980-0.17760.94360.005-0.0089-0.03810.0112-0.0138-0.00330.0088-0.02360.0088-0.1309-0.0536-0.02720.1140.03670.005812.060178.64334.7468
110.61950.24010.17490.101-0.22850.09760.0052-0.0105-0.00450.0029-0.0006-0.01130.0007-0.0118-0.0046-0.0389-0.0329-0.01010.05910.0252-0.022726.34887.007315.8391
120.00350.04610.05450.04720.11170.08020.0004-0.00030.0034-0.0021-0.00090.0011-0.00570.00070.0004-0.0095-0.00210.00990.0221-0.01980.000832.4123105.03810.6074
130.04810.03980.040400.02060.01120.0005-0.0004-0.0008-0.0035-0.0007-0.00110.0008-0.00030.0002-0.0068-0.0086-0.01490.0087-0.0023-0.001133.784288.82929.9572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|0 - A|17 }A0 - 17
2X-RAY DIFFRACTION2{ A|18 - A|53 }A18 - 53
3X-RAY DIFFRACTION3{ A|54 - A|78 }A54 - 78
4X-RAY DIFFRACTION4{ A|79 - A|116 }A79 - 116
5X-RAY DIFFRACTION5{ A|117 - A|143 }A117 - 143
6X-RAY DIFFRACTION6{ A|144 - A|170 }A144 - 170
7X-RAY DIFFRACTION7{ A|171 - A|206 }A171 - 206
8X-RAY DIFFRACTION8{ A|207 - A|236 }A207 - 236
9X-RAY DIFFRACTION9{ A|237 - A|269 }A237 - 269
10X-RAY DIFFRACTION10{ A|270 - A|319 }A270 - 319
11X-RAY DIFFRACTION11{ A|320 - A|343 }A320 - 343
12X-RAY DIFFRACTION12{ A|344 - A|354 }A344 - 354
13X-RAY DIFFRACTION13{ A|401 - A|401 }A401

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