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- PDB-3f6j: F17a-G lectin domain with bound GlcNAc(beta1-3)Gal -

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Basic information

Entry
Database: PDB / ID: 3f6j
TitleF17a-G lectin domain with bound GlcNAc(beta1-3)Gal
ComponentsF17a-G
KeywordsSUGAR BINDING PROTEIN / bacterial adhesion / 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
F17a-G fimbrial adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / 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
DepositionNov 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Dec 17, 2014Group: Atomic model / Derived calculations
Revision 1.4Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 2.0Jul 1, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_asym_id ..._atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_gen.asym_id_list / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 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 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F17a-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4462
Polymers19,0481
Non-polymers3971
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.801, 42.801, 284.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein F17a-G


Mass: 19048.227 Da / Num. of mol.: 1 / Fragment: carbohydrate-binding domain, UNP residues 23-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid details: CUSTOM (T7 promotor) / Plasmid: pHD52 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q99003
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 397.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][a2122h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10%(v/v) 2-propanol, 20%(w/v) PEG 4000, 100mM HEPES, pH 7.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8047 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8047 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 15865 / Num. obs: 15865 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.3 % / Biso Wilson estimate: 17.199 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 16.88
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1366 / % possible all: 90.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9V chain A

1o9v


Resolution: 1.75→32.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.54 / SU ML: 0.083 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 927 5.8 %RANDOM
Rwork0.191 ---
all0.193 14782 --
obs0.193 14782 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.29 Å2 / Biso mean: 17.004 Å2 / Biso min: 8.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0.29 Å20 Å2
2---0.58 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 27 181 1445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221324
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9671813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83824.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56715194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.39155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02990
X-RAY DIFFRACTIONr_nbd_refined0.1980.2561
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.217
X-RAY DIFFRACTIONr_mcbond_it0.7311.5856
X-RAY DIFFRACTIONr_mcangle_it1.2321356
X-RAY DIFFRACTIONr_scbond_it1.7373541
X-RAY DIFFRACTIONr_scangle_it2.5274.5452
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 68 -
Rwork0.242 1028 -
all-1096 -
obs--89.25 %

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