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- PDB-3f64: F17a-G lectin domain with bound GlcNAc(beta1-O)paranitrophenyl ligand -

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Basic information

Entry
Database: PDB / ID: 3f64
TitleF17a-G lectin domain with bound GlcNAc(beta1-O)paranitrophenyl ligand
ComponentsF17a-G
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
Chem-LEC / F17a-G fimbrial adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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. / Weiss, M.S. / Fabre, E. / Guerardel, Y. / Deelder, A.M. / Oscarson, S. / Wuhrer, M. / Bouckaert, J.
History
DepositionNov 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 1, 2020Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Nov 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 1.7Nov 20, 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)19,3912
Polymers19,0481
Non-polymers3421
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)43.025, 43.025, 288.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: pHD52 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q99003
#2: Sugar ChemComp-LEC / 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside / N-[(2S,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-nitrophenoxy)oxan-3-yl]ethanamide / 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucoside / 4-nitrophenyl 2-acetamido-2-deoxy-D-glucoside / 4-nitrophenyl 2-acetamido-2-deoxy-glucoside


Type: D-saccharide / Mass: 342.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2O8
#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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% 2-propanol, 20% PEG 4000, 100mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9183 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2005 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 12042 / Num. obs: 12042 / % possible obs: 94.4 % / Redundancy: 14.7 % / Biso Wilson estimate: 19.008 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 10.2 / Num. unique all: 1105 / % possible all: 91.6

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Processing

Software
NameVersionClassification
MAR345data collection
CNSrefinement
REFMAC5.4.0077refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9V

1o9v


Resolution: 1.95→48.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.965 / SU ML: 0.115 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24845 584 4.9 %RANDOM
Rwork0.20361 ---
obs0.20587 11328 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.376 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 24 181 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221315
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9541796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6452450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54615193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.027156
X-RAY DIFFRACTIONr_chiral_restr0.0840.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021995
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.61.5836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04421344
X-RAY DIFFRACTIONr_scbond_it1.5423479
X-RAY DIFFRACTIONr_scangle_it2.4224.5448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 49 -
Rwork0.217 753 -
obs--91.14 %

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