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- PDB-4gqk: Structure of Native VgrG1-ACD with ADP (no cations) -

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Basic information

Entry
Database: PDB / ID: 4gqk
TitleStructure of Native VgrG1-ACD with ADP (no cations)
ComponentsVgrG protein
KeywordsPROTEIN BINDING / Alpha Beta / Actin cross-linking toxin
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
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar el tor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsNguyen, V.S. / Spinelli, S. / Derrez, E. / Durand, E. / Cambillau, C.
CitationJournal: To be Published
Title: Structure of Native VgrG1-ACD with ADP (no cations)
Authors: Nguyen, V.S. / Spinelli, S. / Derrez, E. / Durand, E. / Cambillau, C.
History
DepositionAug 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 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 / 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 / _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)44,3044
Polymers43,6851
Non-polymers6193
Water7,422412
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)88,6098
Polymers87,3702
Non-polymers1,2396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/41
Buried area4560 Å2
ΔGint-50 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.710, 128.710, 76.590
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: 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 O1 biovar el tor (bacteria)
Strain: N16961 / Gene: VC_1416, VgrG1 / Plasmid: PETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KS45
#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 3.63 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 17, 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: 2.36→50 Å / Num. all: 27021 / Num. obs: 27021 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 34.65 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.1
Reflection shellResolution: 2.36→2.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1923 / % possible all: 97.4

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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: pdb entry 4DTD

4dtd


Resolution: 2.36→46.01 Å / Cor.coef. Fo:Fc: 0.9237 / Cor.coef. Fo:Fc free: 0.8974 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1348 5 %RANDOM
Rwork0.1886 ---
obs0.19 26982 99.76 %-
all-26982 --
Displacement parametersBiso mean: 28.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.0646 Å20 Å20 Å2
2---2.0646 Å20 Å2
3---4.1291 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 2.36→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 37 412 3206
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092932HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.134003HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d01013SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes084HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0434HARMONIC5
X-RAY DIFFRACTIONt_it02932HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion19.26
X-RAY DIFFRACTIONt_chiral_improper_torsion0393SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact03645SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.45 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2666 131 4.73 %
Rwork0.2008 2641 -
all0.2036 2772 -
obs--99.76 %
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)
10.17890.29060.1210.2144-0.08720.0270.0005-0.0024-0.01360.00430.0034-0.01320.00160.0004-0.004-0.0135-0.01250.03190.01580.0038-0.007334.492589.439616.5335
22.0508-0.0901-0.53120.0020.01680.00380.00410.0282-0.02710.02-0.00010.01130.004-0.0068-0.004-0.0574-0.0210.00180.0677-0.0208-0.032546.100690.21976.1002
30.33890.31080.603300.37220.83330.00070.0153-0.0186-0.00880.00170.00490.00730.0035-0.0025-0.06110.0253-0.01130.0823-0.0388-0.023955.11288.284-7.2724
41.0127-0.07381.07850.20630.03310.875600.00470.01180.0284-0.01510.015-0.00160.01460.0151-0.051-0.04420.00260.0507-0.0301-0.035946.477298.828211.2597
51.02230.0337-0.204600.32050.0490.0016-0.0159-0.0031-0.0042-0.0057-0.02120.00330.01440.0041-0.0297-0.02090.00360.0687-0.0175-0.04654.200193.48199.3748
60.0958-0.09110.46460.1081-0.07270.58740.00410.02310.0106-0.015-0.02040.0205-0.01570.02430.0164-0.0317-0.02470.02180.00980.0193-0.023940.766299.35122.7687
70.9108-0.81960.128300.26990.47830.0037-0.02010.0114-0.0050.00570.0054-0.0229-0.0327-0.0094-0.1050.0482-0.00480.0853-0.03030.0059.341991.565213.1418
81.07210.14190.61440.0262-0.62360.09360.005-0.040.0111-0.0352-0.0108-0.01030.0006-0.01410.0058-0.07290.0083-0.02850.05690.01110.00112.434385.96583.9637
90.5810.468-0.97290-0.85231.1239-0.01310.01240.0087-0.00440.0188-0.01330.003-0.0057-0.0057-0.0111-0.0344-0.0130.03170.0147-0.037420.710385.8893-7.254
101.1439-0.1165-0.16110-0.64350.5660.0025-0.0094-0.0442-0.0117-0.00530.00710.0365-0.02990.0028-0.1043-0.0372-0.03540.07480.02220.02711.917178.41474.4089
110.33460.59540.92730.30170.67690.35170.0011-0.0022-0.00590.0015-0.00540.0007-0.0111-0.00550.0043-0.02190.0033-0.01060.03160.0293-0.021326.278886.713715.6763
120-0.00710.05520.17220.10010.08200.00090.0042-0.004-0.0022-0.002-0.01140.00440.0022-0.0092-0.00750.0161-0.0033-0.00760.009632.7739105.35210.6313
130.00270.03740.007300.01670.00390.0004-0.00090.0001-0.0022-0.0007-0.00140.00030.00030.0003-0.0086-0.0122-0.00870.0003-0.0036-0.006233.274788.993210.1456
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|355 }A344 - 355
13X-RAY DIFFRACTION13{ A|401 - A|401 }A401

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