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

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Basic information

Entry
Database: PDB / ID: 4weu
TitleCo-complex structure of the F4 fimbrial adhesin FaeG variant ad with llama single domain antibody V3
Components
  • Anti-F4+ETEC bacteria VHH variable region
  • K88 fimbrial protein AD
KeywordsCELL ADHESION / Complex / Adhesin / Nanobody / Llama single domain antibody
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
K88 fimbrial protein AD / Anti-F4+ETEC bacteria VHH variable region
Similarity search - Component
Biological speciesLama glama (llama)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,5204
Polymers86,5204
Non-polymers00
Water52229
1
D: Anti-F4+ETEC bacteria VHH variable region
B: K88 fimbrial protein AD


Theoretical massNumber of molelcules
Total (without water)43,2602
Polymers43,2602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: K88 fimbrial protein AD
E: Anti-F4+ETEC bacteria VHH variable region


Theoretical massNumber of molelcules
Total (without water)43,2602
Polymers43,2602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.800, 95.200, 113.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21E
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSERDA801 - 9211 - 121
21GLNGLNSERSERED801 - 9211 - 121
12LYSLYSALAALAAB24 - 28516 - 277
22LYSLYSALAALABC24 - 28516 - 277

NCS ensembles :
ID
1
2

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Components

#1: Antibody Anti-F4+ETEC bacteria VHH variable region


Mass: 14042.632 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / References: UniProt: R9W3F6
#2: Protein K88 fimbrial protein AD / K88 antigen / K88 pilin


Mass: 29217.375 Da / Num. of mol.: 2 / Fragment: residues 40-285
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: P14191
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M Ethylene Glycols (Di-Ethyleneglycol; Tri-Ethyleneglycol; TetraEthyleneglycol; Penta-Ethyleneglycol); 0.1 M Tris (base); Bicine pH 8.5; 37.50% % v/v MPD (racemic); PEG 1K; PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.61→29.52 Å / Num. obs: 26553 / % possible obs: 98.3 % / Redundancy: 10.6 % / Net I/σ(I): 16.1
Reflection shellResolution: 2.61→2.67 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.1 / % possible all: 79.6

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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: 2.61→29.54 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 26.18 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.634 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24296 1326 5 %RANDOM
Rwork0.20449 ---
obs0.20643 25194 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0 Å2
2--0.75 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 2.61→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5287 0 0 29 5316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025386
X-RAY DIFFRACTIONr_bond_other_d0.0040.025040
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9447306
X-RAY DIFFRACTIONr_angle_other_deg1311562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2655699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48124.932221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93915836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3931520
X-RAY DIFFRACTIONr_chiral_restr0.0940.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026244
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021240
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_it1.9883.4582829
X-RAY DIFFRACTIONr_mcbond_other1.9873.4582828
X-RAY DIFFRACTIONr_mcangle_it3.0785.1833517
X-RAY DIFFRACTIONr_mcangle_other3.0785.1843518
X-RAY DIFFRACTIONr_scbond_it2.4953.742557
X-RAY DIFFRACTIONr_scbond_other2.493.7412557
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.935.5013790
X-RAY DIFFRACTIONr_long_range_B_refined5.24427.7345612
X-RAY DIFFRACTIONr_long_range_B_other5.24327.7395613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11D6619
12E6619
21A12451
22B12451
LS refinement shellResolution: 2.606→2.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 77 -
Rwork0.33 1465 -
obs--79.44 %
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)
13.81611.87891.05474.2251.36883.55790.05410.1418-0.0567-0.04130.0783-0.197-0.01640.0158-0.13240.02750.0279-0.00690.05980.03260.1276-20.2229-28.926910.3931
24.7880.9632-0.48732.40380.162.488-0.0420.1986-0.1870.22970.04280.1680.1308-0.2724-0.00080.2043-0.0030.00130.0352-0.00390.02975.8885-23.452-15.5029
35.8873-0.9864-0.82394.37860.67083.0516-0.1095-0.56850.01430.21250.3406-0.33550.05920.6849-0.23110.2467-0.04520.02640.2059-0.06740.085410.4942-17.040915.2368
44.2864-1.75662.33944.1689-1.6213.3242-0.0220.1557-0.2418-0.14560.104-0.0460.15820.1692-0.0820.0925-0.0128-0.03480.1435-0.02440.069338.1514-31.114-8.6381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D801 - 921
2X-RAY DIFFRACTION2A24 - 285
3X-RAY DIFFRACTION3B23 - 285
4X-RAY DIFFRACTION4E801 - 921

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