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- PDB-4w6w: Co-complex structure of the lectin domain of F18 fimbrial adhesin... -

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Basic information

Entry
Database: PDB / ID: 4w6w
TitleCo-complex structure of the lectin domain of F18 fimbrial adhesin FedF with inhibitory nanobody NbFedF6
Components
  • F18 fimbrial adhesin AC
  • NbFedF6
KeywordsCELL ADHESION / Adhesin / Inhibitor / Fimbriae
Function / homologyJelly Rolls - #1210 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / F18 fimbrial adhesin AC
Function and homology information
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMoonens, K. / De Kerpel, M. / Annelies, C. / 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 1.2Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_gen.pdbx_host_org_vector_type
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 1.4Nov 6, 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: NbFedF6


Theoretical massNumber of molelcules
Total (without water)30,3972
Polymers30,3972
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint3 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.361, 101.361, 62.768
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein F18 fimbrial adhesin AC / 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 (E. coli) / Gene: fedF / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q47212
#2: Antibody NbFedF6


Mass: 14085.538 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 BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 160 mM NaCl, 80 mM Bis-Tris pH 5.5, 20% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.51→87.8 Å / Num. obs: 13039 / % possible obs: 99.9 % / Redundancy: 10.9 % / Net I/σ(I): 12.6
Reflection shellResolution: 2.51→2.64 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1868 / % possible all: 99.4

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Processing

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

2x1o


Resolution: 2.51→87.78 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.887 / SU B: 17.412 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 633 4.9 %RANDOM
Rwork0.19705 ---
obs0.19974 12390 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å2-0 Å2
2---0.26 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 2.51→87.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 57 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022047
X-RAY DIFFRACTIONr_bond_other_d0.0010.021863
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.9332774
X-RAY DIFFRACTIONr_angle_other_deg0.84934288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7875262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.22724.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68415324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0021510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
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_it0.9831.4851057
X-RAY DIFFRACTIONr_mcbond_other0.9831.4841056
X-RAY DIFFRACTIONr_mcangle_it1.6892.2191316
X-RAY DIFFRACTIONr_mcangle_other1.6882.221317
X-RAY DIFFRACTIONr_scbond_it1.1621.587990
X-RAY DIFFRACTIONr_scbond_other1.1611.587990
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.912.3311459
X-RAY DIFFRACTIONr_long_range_B_refined3.95511.7532153
X-RAY DIFFRACTIONr_long_range_B_other3.93411.7022146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.508→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 63 -
Rwork0.322 863 -
obs--97.89 %
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)
12.37030.9044-0.23.9464-0.82342.4955-0.0559-0.02420.1620.02770.08130.1082-0.1688-0.2233-0.02540.0949-0.0016-0.00620.1627-0.02210.015537.8711-30.4229-15.68
21.88030.95830.20394.26122.65882.4209-0.02590.00030.057-0.0676-0.05420.0018-0.1618-0.02130.08010.15180.0074-0.0020.14020.03230.047757.5081-13.509-22.8411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 161
2X-RAY DIFFRACTION2B802 - 925

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