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- PDB-4dtd: Structure and functional characterization of a Vibrio cholerae to... -

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Basic information

Entry
Database: PDB / ID: 4dtd
TitleStructure and functional characterization of a Vibrio cholerae toxin from the MARTX/VgrG family.
ComponentsVgrG protein
KeywordsTOXIN / Alpha-Beta protein / Actin Crosslinking Domain (ACD) / 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 / 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
Actin cross-linking toxin VgrG1 / Actin cross-linking toxin VgrG1
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 a Vibrio cholerae toxin from the MARTX/VgrG family.
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

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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)44,2562
Polymers44,1641
Non-polymers921
Water2,882160
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)88,5134
Polymers88,3292
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/41
Buried area3110 Å2
ΔGint-8 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.080, 128.080, 76.520
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: 44164.270 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
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 293 K / pH: 6.3
Details: mixing 300 nL of protein at 13mg/mL with 100 nL of 2.17 M AmSO4, 0.1 M Bi-Tris pH 7.0 , 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: Dec 16, 2011
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: 2.5→49.1 Å / Num. obs: 22710 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 17.3 % / Biso Wilson estimate: 64.05 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.2
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 17 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 5 / % possible all: 99.5

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.86 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1154 5.11 %RANDOM
Rwork0.187 ---
obs0.188 22605 --
all-22605 --
Displacement parametersBiso mean: 62.24 Å2
Baniso -1Baniso -2Baniso -3
1--10.0066 Å20 Å20 Å2
2---10.0066 Å20 Å2
3---20.0131 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 6 160 2935
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012857HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.183882HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d985SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes408HARMONIC5
X-RAY DIFFRACTIONt_it2857HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion20.15
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_contact03396SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.62 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.29 144 4.87 %
Rwork0.2109 2810 -
all0.2146 2954 -
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)
10.1490.0302-0.00920-0.08200.00040.00130.00070.004-0.0005-0.00030.0021-0.00080.00010.0019-0.0009-0.00110.00940.00350.004534.985485.25088.3804
22.5381-0.1072-0.092300.315800.0077-0.0053-0.03890.03290.01650.00880.0015-0.0346-0.0242-0.0762-0.05340.00240.0383-0.0010.009242.112790.53019.7313
30.40760.56940.45680.49550.4870.9341-0.00080.0185-0.0156-0.0158-0.00560.0077-0.0009-0.01040.0064-0.05910.0487-0.06360.0507-0.08190.023655.124587.4681-8.0717
40.4154-1.14130.61220.3304-0.20861.1583-0.0001-0.04920.0145-0.0013-0.0083-0.0134-0.0046-0.06290.0083-0.0704-0.01320.04670.0501-0.0338-0.005144.878198.614811.8132
51.51-0.81490.20010.00020.590400.007-0.0235-0.02170.0072-0.0128-0.0032-0.00110.0040.0058-0.02910.0054-0.04960.0225-0.05840.010354.784892.82689.132
60.8305-0.14642.32960.2844-1.13141.30050.0041-0.00490.0278-0.0066-0.0115-0.0127-0.0028-0.02860.0074-0.06040.03680.02850.02930.0432-0.017543.351199.78390.6172
70.8541-0.4275-0.743400.16440.84660.003-0.0040.0104-0.0066-0.00230.01150.0030.0078-0.0007-0.13190.04760.04860.16250.016-0.028210.08191.310112.9354
82.1316-1.66441.25020.2171-1.43220.22380.0101-0.0041-0.00240.02-0.02170.00560.018-0.00630.0116-0.10580.07990.00840.11990.0699-0.024610.928185.05546.3434
91.0961-0.4344-0.67580.01730.77230.1146-0.0008-0.0004-0.0183-0.0023-0.0018-0.0080.01080.01350.0026-0.07260.13620.01250.10750.0459-0.033920.007985.1268-8.5924
101.1891-0.9801-0.78630-0.90870.90830.00650.0056-0.02550.0155-0.01950.00820.045-0.01060.013-0.07030.09980.02140.11280.0968-0.040312.055977.98824.7985
111.2825-0.49930.08480-0.812100.00470.022-0.00240.0174-0.0071-0.00540.0153-0.00560.0024-0.02850.0417-0.01830.08280.0629-0.049326.298784.526815.6485
120.1073-0.12320.05220.0152-0.01130.0784-0.0003-0.0020.0016-0.0010.00130.001-0.0047-0.0014-0.001-0.01430.02470.00220.02440.0067-0.002731.2556104.1539.824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 10 A 17
2X-RAY DIFFRACTION2A 18 A 63
3X-RAY DIFFRACTION3A 64 A 88
4X-RAY DIFFRACTION4A 89 A 126
5X-RAY DIFFRACTION5A 127 A 153
6X-RAY DIFFRACTION6A 154 A 180
7X-RAY DIFFRACTION7A 181 A 216
8X-RAY DIFFRACTION8A 217 A 246
9X-RAY DIFFRACTION9A 247 A 279
10X-RAY DIFFRACTION10A 280 A 329
11X-RAY DIFFRACTION11A 330 A 353
12X-RAY DIFFRACTION12A 354 A 354

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