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- PDB-4w6y: Co-complex structure of the lectin domain of F18 fimbrial adhesin... -

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Basic information

Entry
Database: PDB / ID: 4w6y
TitleCo-complex structure of the lectin domain of F18 fimbrial adhesin FedF with inhibitory nanobody NbFedF9
Components
  • F18 fimbrial adhesin AC
  • Nanobody NbFedF9
KeywordsCELL ADHESION / Adhesin / Fimbriae / Inhibitor
Function / homologyJelly Rolls - #1210 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / F18 fimbrial adhesin AC
Function and homology information
Biological speciesEscherichia coli DH5[alpha] (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMoonens, K. / De Kerpel, M. / Coddens, A. / Cox, E. / Pardon, E. / Remaut, H. / De Greve, H.
Funding support Belgium, 2items
OrganizationGrant numberCountry
FWOG030411N Belgium
FWO - HerculesUABR/09/005 Belgium
CitationJournal: Plos One / Year: 2014
Title: Nanobody Mediated Inhibition of Attachment of F18 Fimbriae Expressing Escherichia coli.
Authors: Moonens, K. / De Kerpel, M. / Coddens, A. / Cox, E. / Pardon, E. / Remaut, H. / De Greve, H.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 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 1.4Oct 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: F18 fimbrial adhesin AC
B: Nanobody NbFedF9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5856
Polymers31,2002
Non-polymers3844
Water4,107228
1
A: F18 fimbrial adhesin AC
B: Nanobody NbFedF9
hetero molecules

A: F18 fimbrial adhesin AC
B: Nanobody NbFedF9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,16912
Polymers62,4014
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6370 Å2
ΔGint-114 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.562, 102.961, 114.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-358-

HOH

21B-335-

HOH

31B-338-

HOH

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Components

#1: Protein F18 fimbrial adhesin AC / FedF / Lectin domain of F18 fimbrial adhesin FedF


Mass: 16311.161 Da / Num. of mol.: 1 / Fragment: UNP Residues 35-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Gene: fedF / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: Q47212
#2: Antibody Nanobody NbFedF9


Mass: 14889.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pDESTR4-R3 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2 M (NH4)2 SO4, 5% PEG-400 and 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→46.95 Å / Num. obs: 42810 / % possible obs: 98.6 % / Redundancy: 9.7 % / Net I/σ(I): 11.1
Reflection shellResolution: 1.57→1.66 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.837 / Mean I/σ(I) obs: 1 / Num. unique all: 5989 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B4P and 2X1O

4b4p

2x1o


Resolution: 1.57→57.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.455 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22567 2157 5 %RANDOM
Rwork0.19497 ---
obs0.19648 40616 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.383 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.57→57.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 20 228 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192295
X-RAY DIFFRACTIONr_bond_other_d0.0010.022028
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.9333147
X-RAY DIFFRACTIONr_angle_other_deg0.913.0014683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26824.24299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89915362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4351513
X-RAY DIFFRACTIONr_chiral_restr0.1340.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022762
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02565
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_it1.1921.2561181
X-RAY DIFFRACTIONr_mcbond_other1.1871.2551180
X-RAY DIFFRACTIONr_mcangle_it1.7981.8721503
X-RAY DIFFRACTIONr_mcangle_other1.7981.8731504
X-RAY DIFFRACTIONr_scbond_it2.1131.5221114
X-RAY DIFFRACTIONr_scbond_other2.0071.4761098
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0352.1341620
X-RAY DIFFRACTIONr_long_range_B_refined6.39411.7552613
X-RAY DIFFRACTIONr_long_range_B_other6.10711.0042511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.574→1.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.559 148 -
Rwork0.506 2792 -
obs--92.86 %
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)
11.44780.092-0.00842.44120.06270.96260.0285-0.1461-0.11340.2033-0.05230.23080.0810.00210.02380.0271-0.00440.01860.01640.00720.0325-0.9888-3.84812.9546
24.57180.0153-1.81870.64490.08632.19420.1701-0.09460.29540.0729-0.009-0.0434-0.1004-0.0072-0.16110.06290.003-0.00040.0042-0.00540.0243-19.950413.9711.3171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 161
2X-RAY DIFFRACTION2B1 - 128

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