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- PDB-4wen: Co-complex structure of the F4 fimbrial adhesin FaeG variant ac w... -

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Basic information

Entry
Database: PDB / ID: 4wen
TitleCo-complex structure of the F4 fimbrial adhesin FaeG variant ac with llama single domain antibody V2
Components
  • Anti-F4+ETEC bacteria VHH variable region
  • K88 fimbrial protein AC
KeywordsSTRUCTURAL PROTEIN / Complex / Adhesin / Llama single domain antibody / Nanobody
Function / homology
Function and homology information


pilus / immunoglobulin complex / adaptive immune response / cell adhesion / extracellular region
Similarity search - Function
Fimbrial, major/minor subunit / Fimbrial, major and minor subunit / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Fimbrial, major/minor subunit / Fimbrial, major and minor subunit / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
K88 fimbrial protein AC / K88 fimbrial protein AC / Anti-F4+ETEC bacteria VHH variable region
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMoonens, K. / Van den Broeck, I. / Pardon, E. / De Kerpel, M. / Remaut, H. / De Greve, H.
Funding support Belgium, 2items
OrganizationGrant numberCountry
FWOG030411N Belgium
FWO - HerculesUABR/09/005 Belgium
Citation
Journal: Vet. Res. / Year: 2015
Title: Structural insight in the inhibition of adherence of F4 fimbriae producing enterotoxigenic Escherichia coli by llama single domain antibodies.
Authors: Moonens, K. / Van den Broeck, I. / Okello, E. / Pardon, E. / De Kerpel, M. / Remaut, H. / De Greve, H.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: Orally fed seeds producing designer IgAs protect weaned piglets against enterotoxigenic Escherichia coli infection.
Authors: Virdi, V. / Coddens, A. / De Buck, S. / Millet, S. / Goddeeris, B.M. / Cox, E. / De Greve, H. / Depicker, A.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Jan 10, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: K88 fimbrial protein AC
B: Anti-F4+ETEC bacteria VHH variable region


Theoretical massNumber of molelcules
Total (without water)42,7482
Polymers42,7482
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-3 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.833, 145.833, 37.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein K88 fimbrial protein AC


Mass: 28993.223 Da / Num. of mol.: 1 / Fragment: UNP residues 20-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: faeG / Plasmid: pDEST14 / Details (production host): Gateway technology / Production host: Escherichia coli (E. coli) / References: UniProt: L7XD53, UniProt: P14190*PLUS
#2: Antibody Anti-F4+ETEC bacteria VHH variable region


Mass: 13754.295 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) / References: UniProt: R9VYW2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM Sodium Acetate pH 4.6, 200 mM ammonium sulfate, 25 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.89→47.74 Å / Num. obs: 36784 / % possible obs: 99.7 % / Redundancy: 20.2 % / Net I/σ(I): 14.3
Reflection shellResolution: 1.89→2 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 1.4 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLR

3hlr


Resolution: 1.89→47.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.867 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22599 1837 5 %RANDOM
Rwork0.18819 ---
obs0.19016 34871 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.539 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0.69 Å2-0 Å2
2---1.38 Å20 Å2
3---4.49 Å2
Refinement stepCycle: 1 / Resolution: 1.89→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 0 105 2854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022799
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.9463799
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5785372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10424.537108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2415441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8571513
X-RAY DIFFRACTIONr_chiral_restr0.1580.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212091
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4642.6111494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4633.8871861
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3742.8811304
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.15322.5754138
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 108 -
Rwork0.36 2360 -
obs--92.5 %
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)
15.0442.54451.77513.2061.15591.7872-0.33470.4247-0.1368-0.44540.1934-0.0545-0.0157-0.17790.14130.1795-0.07530.07570.1304-0.07010.055651.6249-17.29317.0392
23.53491.748-0.99515.3617-0.96253.62530.1303-0.362-0.32320.2804-0.1737-0.77780.25630.09570.04340.1709-0.0514-0.02410.055-0.01140.317251.0313-37.9623.3211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 283
2X-RAY DIFFRACTION2B801 - 921

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