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

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Basic information

Entry
Database: PDB / ID: 4dth
TitleStructure of a VgrG Vibrio cholerae toxin ACD domain in complex with ATP and Mg++
ComponentsVgrG protein
KeywordsTOXIN / alpha-beta protein / actin cross-linking toxin / G-actin
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
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'-TRIPHOSPHATE / Actin cross-linking toxin VgrG1 / Actin cross-linking toxin VgrG1
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 of a VgrG Vibrio cholerae toxin ACD domain in complex with ATP and Mg++
Authors: Durand, E. / Audoly, G. / Derrez, E. / Spinelli, S. / Ortiz-Lombardia, M. / Cascales, E. / Raoult, D. / Cambillau, C.
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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

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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)44,87010
Polymers43,7421
Non-polymers1,1289
Water10,233568
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)89,74120
Polymers87,4842
Non-polymers2,25618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/41
Buried area7460 Å2
ΔGint-188 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.680, 128.680, 76.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein VgrG protein


Mass: 43742.215 Da / Num. of mol.: 1 / Fragment: unp residues 716-1111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: VC_1416, VgrG1 / Plasmid: pETG-20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KS45, UniProt: A0A0H3AIG7*PLUS

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Non-polymers , 5 types, 577 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-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


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


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


Mass: 18.015 Da / Num. of mol.: 568 / 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: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 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 pH 6,3. , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2012
Details: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationMonochromator: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 62298 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 27.67 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.5
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→46.06 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1883 3.03 %RANDOM
Rwork0.181 ---
obs0.181 62135 99.9 %-
all-62135 --
Displacement parametersBiso mean: 32.84 Å2
Baniso -1Baniso -2Baniso -3
1--3.3002 Å20 Å20 Å2
2---3.3002 Å20 Å2
3---6.6003 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.78→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 64 568 3389
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092949HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014027HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1017SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes434HARMONIC5
X-RAY DIFFRACTIONt_it2949HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion18.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion0393SEMIHARMONIC5
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_contact03898SEMIHARMONIC4
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2467 131 2.89 %
Rwork0.2155 4400 -
all0.2165 4531 -
obs--99.94 %
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)
10.34340.27510.23380-0.26130.03690.0028-0.0032-0.00330.0101-0.0012-0.010.0107-0.0082-0.0016-0.0318-0.02890.03660.05140.0141-0.015834.490689.250216.6126
21.4307-0.0632-0.45700.08430.03440.0055-0.0079-0.0310.0037-0.00750.0070.0088-0.0060.002-0.0476-0.01410.01010.0540.012-0.015846.084890.03886.2749
30.28530.14390.1540.16530.20350.71170.00170.0107-0.0126-0.00210.00880.00320.00590.0033-0.0105-0.05510.01080.00430.0621-0.0474-0.003955.049688.1179-7.1972
40.4576-0.07310.55320.34680.08160.6675-0.0016-0.01940.01750.026-0.0193-0.0081-0.0011-0.01520.0209-0.0559-0.03420.00850.05850.0026-0.024646.495298.621811.3384
51.0195-0.0446-0.10820.0050.25110.04230.0017-0.0172-0.00560.0029-0.00880.00510.00080.00940.007-0.0393-0.0047-0.00080.06630.0021-0.026354.145293.27959.4957
60.23860.08050.45610.16550.00320.4726-0.0026-0.00130.01330.0033-0.0040.013-0.0222-0.00020.0066-0.0364-0.01350.02360.02650.0083-0.014340.73999.14382.8176
70.6619-0.2402-0.445200.17360.57090.0026-0.01710.00620.01460.00410.0068-0.0126-0.0109-0.0067-0.10370.0340.01440.1041-0.0494-0.00649.294191.346313.2065
80.98050.3310.2720.2085-0.09750.09650.0019-0.04640.0056-0.0222-0.00310.00340.0002-0.0210.0013-0.10230.01070.00150.0859-0.00350.00612.418385.75244.0131
90.84330.1717-0.74860.0183-0.19960.4801-0.01080.0030.0062-0.02170.0128-0.00710.02170.0013-0.002-0.04880.0069-0.01610.06470.0253-0.023820.744185.7852-7.2003
101.0616-0.3286-0.34110-0.16510.8260.007-0.0144-0.04620.0069-0.0143-0.00360.0296-0.02360.0073-0.1185-0.0197-0.01710.10030.01750.013511.941478.20934.3797
110.48870.1110.3150.0833-0.11510.11420.0068-0.0006-0.00160.0135-0.0028-0.00660.0061-0.0074-0.004-0.0409-0.0194-0.0140.07310.0272-0.030126.23186.570715.7554
120.0187-0.0269-0.01240.09970.17050.0816-0.0004-0.00360.003-0.0037-0.00160.0031-0.0073-0.00190.002-0.0107-0.00070.02430.0183-0.01720.000832.7734105.15910.6926
130.02680.03370.011100.028500.0004-0.0021-0.0012-0.0023-0.0007-0.00070.0013-0.00010.0002-0.0085-0.0066-0.00320.00640.0021-0.003332.9588.25089.2754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 0 A 17
2X-RAY DIFFRACTION2A 18 A 53
3X-RAY DIFFRACTION3A 54 A 78
4X-RAY DIFFRACTION4A 79 A 116
5X-RAY DIFFRACTION5A 117 A 143
6X-RAY DIFFRACTION6A 144 A 170
7X-RAY DIFFRACTION7A 171 A 206
8X-RAY DIFFRACTION8A 207 A 236
9X-RAY DIFFRACTION9A 237 A 269
10X-RAY DIFFRACTION10A 270 A 319
11X-RAY DIFFRACTION11A 320 A 343
12X-RAY DIFFRACTION12A 344 A 355
13X-RAY DIFFRACTION13A 401 A 401

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