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- PDB-3ffo: F17b-G lectin domain with bound GlcNAc(beta1-2)man -

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Basic information

Entry
Database: PDB / ID: 3ffo
TitleF17b-G lectin domain with bound GlcNAc(beta1-2)man
ComponentsAdhesin
KeywordsSUGAR BINDING PROTEIN / bacterial adhesin / lectin / bacterial attachment / pathogenesis / immunoglobulin fold / Cell projection / Fimbrium
Function / homology
Function and homology information


adhesion of symbiont to host / cell adhesion involved in single-species biofilm formation / pilus / carbohydrate binding
Similarity search - Function
Bacterial adhesins - F17c-type / Fimbrial adhesin F17-AG, lectin domain / Fimbrial adhesin F17-AG, lectin domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / F17b-G fimbrial adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsButs, L. / De Boer, A. / Olsson, J.D.M. / Jonckheere, W. / De Kerpel, M. / De Genst, E. / Guerardel, Y. / Willaert, R. / Wyns, L. / Wuhrer, M. ...Buts, L. / De Boer, A. / Olsson, J.D.M. / Jonckheere, W. / De Kerpel, M. / De Genst, E. / Guerardel, Y. / Willaert, R. / Wyns, L. / Wuhrer, M. / Oscarson, S. / De Greve, H. / Bouckaert, J.
CitationJournal: Biology (Basel) / Year: 2013
Title: Structural Sampling of Glycan Interaction Profiles Reveals Mucosal Receptors for Fimbrial Adhesins of Enterotoxigenic Escherichia coli.
Authors: Lonardi, E. / Moonens, K. / Buts, L. / de Boer, A.R. / Olsson, J.D.M. / Weiss, M.S. / Fabre, E. / Guerardel, Y. / Deelder, A.M. / Oscarson, S. / Wuhrer, M. / Bouckaert, J.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 28, 2013Group: Database references / Non-polymer description
Revision 1.3Dec 17, 2014Group: Atomic model / Database references / Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 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: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6536
Polymers18,8971
Non-polymers7565
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.389, 87.389, 56.809
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-263-

NI

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Adhesin


Mass: 18896.871 Da / Num. of mol.: 1 / Fragment: carbohydrate-binding domain, residues 23-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: F17b-G / Plasmid: pHD52 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q47200
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 51 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 1.2M lithium sulphate, 10mM nickel chloride, 100mM TRIS, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8453 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 14544 / Num. obs: 14544 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 43.42 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.6 / Num. unique all: 1463 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: 1O9V

1o9v


Resolution: 2.1→18.92 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.748 / SU ML: 0.42 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / σ(I): 0 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1474 10.16 %random
Rwork0.233 ---
all0.237 14511 --
obs0.237 14511 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.712 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 102.42 Å2 / Biso mean: 49.846 Å2 / Biso min: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1-3.082 Å2-0 Å2-0 Å2
2--3.082 Å2-0 Å2
3----6.163 Å2
Refinement stepCycle: LAST / Resolution: 2.1→18.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 45 47 1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051388
X-RAY DIFFRACTIONf_angle_d0.971889
X-RAY DIFFRACTIONf_chiral_restr0.059211
X-RAY DIFFRACTIONf_plane_restr0.003241
X-RAY DIFFRACTIONf_dihedral_angle_d18.309479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1680.3061230.2791176129999
2.168-2.2450.3671170.27812011318100
2.245-2.3350.3891420.30311681310100
2.335-2.4410.3851390.30411661305100
2.441-2.5690.371350.3111801315100
2.569-2.730.3731660.30111471313100
2.73-2.940.3341310.28211851316100
2.94-3.2340.3391260.26411931319100
3.234-3.6990.2621170.22112031320100
3.699-4.6490.2121550.18411751330100
4.649-18.9210.1791230.17812431366100

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