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- PDB-5mwn: Structure of the EAEC T6SS component TssK N-terminal domain in co... -

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Basic information

Entry
Database: PDB / ID: 5mwn
TitleStructure of the EAEC T6SS component TssK N-terminal domain in complex with llama nanobodies nbK18 and nbK27
Components
  • Type VI secretion protein
  • llama nanobody raised against TssK, nbK18
  • llama nanobody raised against TssK, nbK27
KeywordsTRANSPORT PROTEIN / Type 6 secretion system component TssK N-terminal domain with llama nanobodies nbK18 and nbK27
Function / homologyBacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / Type VI secretion system TssK / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION / Type VI secretion protein / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCambillau, C. / Nguyen, V.S. / Spinelli, S. / Legrand, P.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE14-0006-02 France
French National Research AgencyFRISBI 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
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jul 19, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: llama nanobody raised against TssK, nbK18
E: llama nanobody raised against TssK, nbK18
F: llama nanobody raised against TssK, nbK18
N: llama nanobody raised against TssK, nbK27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,9538
Polymers161,8597
Non-polymers951
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24500 Å2
ΔGint-176 kcal/mol
Surface area55180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.310, 150.280, 90.840
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


Mass: 35703.809 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 BL21 (bacteria) / References: UniProt: A0A0P7QEP7, UniProt: A0A0N8J9U9*PLUS
#2: Antibody llama nanobody raised against TssK, nbK18


Mass: 13705.288 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody llama nanobody raised against TssK, nbK27


Mass: 13631.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 45% PEG600, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 100494 / % possible obs: 95.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 57.31 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / Num. unique obs: 16357 / CC1/2: 0.5 / % possible all: 92.4

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M30

5m30


Resolution: 2.2→45.03 Å / Cor.coef. Fo:Fc: 0.9513 / Cor.coef. Fo:Fc free: 0.9438 / SU R Cruickshank DPI: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.167
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 5032 5.12 %RANDOM
Rwork0.1988 ---
obs0.1999 98369 98.33 %-
Displacement parametersBiso mean: 66.39 Å2
Baniso -1Baniso -2Baniso -3
1-4.5506 Å20 Å20 Å2
2--4.3639 Å20 Å2
3----8.9145 Å2
Refine analyzeLuzzati coordinate error obs: 0.323 Å
Refinement stepCycle: 1 / Resolution: 2.2→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10822 0 5 699 11526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811067HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0715097HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3696SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes250HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1638HARMONIC5
X-RAY DIFFRACTIONt_it11067HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion19.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1426SEMIHARMONIC5
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_contact12409SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 331 4.79 %
Rwork0.2323 6573 -
all0.2331 6904 -
obs--98.33 %
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)
10.4309-0.0186-0.30080.50840.13130.47030.0214-0.0954-0.0826-0.0235-0.0712-0.00230.08350.01810.0498-0.0521-0.0378-0.0176-0.08750.05420.054410.397-41.9473-11.1579
20.048-0.08640.03090.71870.19960.43450.00540.02810.00920.0378-0.0288-0.07840.00750.13280.0233-0.1175-0.0329-0.01150.03990.03160.005232.5129-25.9238-12.2701
30.6506-0.05-0.34380.57280.34820.60670.01520.09470.0435-0.1033-0.01480.10490.0234-0.014-0.00040.0013-0.0199-0.0315-0.06670.043-0.035112.2573-22.2668-30.3111
40.14070.57660.04110.7071-0.89371.9657-0.004-0.0386-0.00050.02960.02260.00450.0374-0.0078-0.01860.0156-0.0112-0.0304-0.0121-0.0182-0.053329.5477-26.382527.2687
51.80340.3699-0.43581.2122-0.89730.415-0.00630.0270.043-0.0101-0.01350.0353-0.0424-0.00440.0198-0.075-0.06350.0259-0.0525-0.03160.0874-27.9281-31.3046-7.6507
61.06570.53390.45211.4825-1.16160.53330.0142-0.0526-0.00070.0373-0.0433-0.0224-0.016-0.01060.0292-0.06150.02130.0253-0.06610.05640.073516.452816.6923-23.9524
70.05520.4099-0.655200.95250.0844-0.0028-0.02560.0020.04130.0120.0015-0.0185-0.012-0.0092-0.0246-0.0020.04890.0158-0.03080.0044-8.3758-2.353820.1836
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|* }
7X-RAY DIFFRACTION7{ N|* }

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