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- PDB-5m30: Structure of TssK from T6SS EAEC in complex with nanobody nb18 -

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Basic information

Entry
Database: PDB / ID: 5m30
TitleStructure of TssK from T6SS EAEC in complex with nanobody nb18
Components
  • Anti-vesicular stomatitis virus N VHH
  • Type VI secretion proteinType VI secretion system
KeywordsSECRETION SYSTEM / TssK T6SS
Function / homologyType VI secretion system TssK / Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / Type VI secretion protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNguyen, V.S. / Cambillau, C. / Spinelli, C. / Desmyter, A. / Legrand, P. / Cascales, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR- 14-CE14-0006-01 France
CitationJournal: Nat Microbiol / Year: 2017
Title: Type VI secretion TssK baseplate protein exhibits structural similarity with phage receptor-binding proteins and evolved to bind the membrane complex.
Authors: Nguyen, V.S. / Logger, L. / Spinelli, S. / Legrand, P. / Huyen Pham, T.T. / Nhung Trinh, T.T. / Cherrak, Y. / Zoued, A. / Desmyter, A. / Durand, E. / Roussel, A. / Kellenberger, C. / Cascales, E. / Cambillau, C.
History
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.title / _citation.year
Revision 1.2Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type VI secretion protein
B: Type VI secretion protein
C: Type VI secretion protein
D: Anti-vesicular stomatitis virus N VHH
E: Anti-vesicular stomatitis virus N VHH
F: Anti-vesicular stomatitis virus N VHH


Theoretical massNumber of molelcules
Total (without water)191,1146
Polymers191,1146
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-80 kcal/mol
Surface area57660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.240, 153.670, 154.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type VI secretion protein / Type VI secretion system


Mass: 49999.223 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ACU81_04625 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0P7QEP7, UniProt: D3GU39*PLUS
#2: Antibody Anti-vesicular stomatitis virus N VHH


Mass: 13705.288 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Complex at 10 mg per ml mixes to 0.2 MgCl2, 10 % PEK 6000, 0.1 M Tris pH 8.3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 69265 / % possible obs: 99.8 % / Redundancy: 11 % / Biso Wilson estimate: 108.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 19.6
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 0.5 / CC1/2: 0.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.92 Å / Cor.coef. Fo:Fc: 0.9449 / Cor.coef. Fo:Fc free: 0.9321 / SU R Cruickshank DPI: 0.426 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.422 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 2988 5 %RANDOM
Rwork0.2069 ---
obs0.2079 59771 86.53 %-
Displacement parametersBiso mean: 106.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.5588 Å20 Å20 Å2
2---0.4359 Å20 Å2
3----0.1229 Å2
Refine analyzeLuzzati coordinate error obs: 0.451 Å
Refinement stepCycle: 1 / Resolution: 2.6→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10123 0 0 208 10331
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110345HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2114120HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3415SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes218HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1535HARMONIC5
X-RAY DIFFRACTIONt_it10345HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion21.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1352SEMIHARMONIC5
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_contact11025SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2968 48 4.55 %
Rwork0.2402 1007 -
all0.2428 1055 -
obs--86.53 %
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)
10.59750.76230.48621.68610.37930.38190.00550.0059-0.01250.08180.03770.0702-0.0427-0.0872-0.0433-0.05790.04730.0247-0.0774-0.08720.064635.20110.4748103.111
20.15710.48650.63690.41510.39081.1072-0.0324-0.0239-0.06270.02310.02190.03560.02740.00730.01050.0330.0504-0.0329-0.0627-0.14640.008348.1753-20.817690.6789
31.87180.3881-0.06640.379-0.06630.63330.0130.0430.0648-0.1092-0.03250.00630.0021-0.02890.0194-0.0420.0259-0.070.0651-0.0231-0.098456.160210.021180.8731
40-0.8262-0.84070.75260.22941.99410.0119-0.04220.0132-0.0205-0.02640.039-0.05410.00580.01450.04030.02930.00140.0437-0.0942-0.074457.46580.9007142.075
50-0.341-0.57051.4446-0.65360.6935-0.00810.0271-0.0052-0.0201-0.0108-0.037-0.00350.03720.01890.0522-0.03860.0294-0.0101-0.0168-0.016546.631751.6869103.578
61.7029-0.73620.54680-0.5031.10630.0001-0.01280.0328-0.00360.0215-0.04670.0198-0.0175-0.0216-0.115-0.021-0.01060.05040.07130.059696.83038.140791.9561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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