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- PDB-5m2w: Structure of nanobody nb18 raised against TssK from E. coli T6SS -

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Basic information

Entry
Database: PDB / ID: 5m2w
TitleStructure of nanobody nb18 raised against TssK from E. coli T6SS
ComponentsLlama nanobody nb8 against TssK from T6SS
KeywordsIMMUNE SYSTEM / T6SS TssK nanobody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCambillau, C. / Nguyen, V.S. / Spinelli, S. / Desmyter, A.
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 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 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Llama nanobody nb8 against TssK from T6SS
B: Llama nanobody nb8 against TssK from T6SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6995
Polymers27,4112
Non-polymers2883
Water5,242291
1
A: Llama nanobody nb8 against TssK from T6SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8012
Polymers13,7051
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Llama nanobody nb8 against TssK from T6SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8973
Polymers13,7051
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.390, 53.390, 88.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Antibody Llama nanobody nb8 against TssK from T6SS


Mass: 13705.288 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: 100 nL of 13 mg per ml nb18 protein solution with 100 nL of 0.2 M Li2SO4, 0.1 M NaAc pH 4.75, 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 38858 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.67 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.8
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.61 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→12.1 Å / Cor.coef. Fo:Fc: 0.9542 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1940 5 %RANDOM
Rwork0.2026 ---
obs0.2032 38782 98.55 %-
Displacement parametersBiso mean: 28.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.8397 Å20 Å20 Å2
2---0.8397 Å20 Å2
3---1.6794 Å2
Refine analyzeLuzzati coordinate error obs: 0.239 Å
Refinement stepCycle: 1 / Resolution: 1.5→12.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 15 291 2089
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081832HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12490HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d617SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes280HARMONIC5
X-RAY DIFFRACTIONt_it1832HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion14.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion236SEMIHARMONIC5
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_contact2210SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2871 146 5.02 %
Rwork0.3057 2762 -
all0.3048 2908 -
obs--98.55 %
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)
11.361-0.3561-0.2051.6422-1.50941.3723-0.0049-0.0196-0.00360.01870.03940.02840.0777-0.0063-0.0344-0.0425-0.0111-0.061-0.01130.0178-0.02013.37711.45760.012
21.7747-0.54350.61421.1796-0.0061.1576-0.02190.0073-0.0346-0.0320.0142-0.0023-0.1006-0.04280.0078-0.0197-0.0305-0.0261-0.0170.0408-0.0288-13.372830.0848-16.1391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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