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

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Basic information

Entry
Database: PDB / ID: 4wem
TitleCo-complex structure of the F4 fimbrial adhesin FaeG variant ac with llama single domain antibody V1
Components
  • Anti-F4+ETEC bacteria VHH variable region
  • K88 fimbrial protein AC
KeywordsSTRUCTURAL PROTEIN / Complex / llama single domain antibody / adhesin / nanobody
Function / homology
Function and homology information


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 / Immunoglobulins / Immunoglobulin-like fold ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / 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: 1.55 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,0626
Polymers42,6822
Non-polymers3804
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-25 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.483, 145.483, 38.847
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein K88 fimbrial protein AC


Mass: 28703.873 Da / Num. of mol.: 1
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: 13978.585 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: R9W2R6
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Potassium bromide, 0.1 M Sodium acetate pH 5.5, 15 % 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: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→47.62 Å / Num. obs: 68481 / % possible obs: 99.9 % / Redundancy: 11.2 % / Net I/σ(I): 24.8
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 4.2 / % possible all: 99

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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: 1.55→47.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.666 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19326 3467 5.1 %RANDOM
Rwork0.16882 ---
obs0.17008 65014 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.314 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å2-0 Å2
2---0.19 Å20 Å2
3---0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.55→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 20 304 3072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192846
X-RAY DIFFRACTIONr_bond_other_d0.0010.022677
X-RAY DIFFRACTIONr_angle_refined_deg2.7151.9493864
X-RAY DIFFRACTIONr_angle_other_deg1.02336137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22424.545121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69215453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3311515
X-RAY DIFFRACTIONr_chiral_restr0.1360.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023309
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
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_it1.8141.571483
X-RAY DIFFRACTIONr_mcbond_other1.8151.5681482
X-RAY DIFFRACTIONr_mcangle_it2.5972.3411848
X-RAY DIFFRACTIONr_mcangle_other2.5972.3431849
X-RAY DIFFRACTIONr_scbond_it3.0211.9381362
X-RAY DIFFRACTIONr_scbond_other2.9831.9161346
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4162.7521987
X-RAY DIFFRACTIONr_long_range_B_refined7.61415.0393330
X-RAY DIFFRACTIONr_long_range_B_other7.55214.073180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.549→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 258 -
Rwork0.234 4739 -
obs--99.13 %
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)
13.56111.48511.54171.92531.32922.0308-0.1950.17630.0492-0.3190.03090.1253-0.1847-0.16550.16410.0959-0.0112-0.00810.0584-0.02120.019951.9517-16.7834-12.2805
20.47811.078-0.64295.137-0.51992.97510.0316-0.1811-0.17290.1789-0.1208-0.17980.17250.0570.08920.0575-0.0349-0.01090.15610.10040.145551.2057-37.55793.7071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 290
2X-RAY DIFFRACTION2B801 - 921

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