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- PDB-1o9w: F17-aG lectin domain from Escherichia coli in complex with N-acet... -

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Basic information

Entry
Database: PDB / ID: 1o9w
TitleF17-aG lectin domain from Escherichia coli in complex with N-acetyl-glucosamine
ComponentsF17A-G FIMBRIAL ADHESIN
KeywordsSUGAR BINDING PROTEIN / BACTERIAL ADHESIN / BACTERIAL ATTACHMENT / SUGAR BINDING PROTEIN PATHOGENESIS / IMMUNOGLOBULIN FOLD
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: 1.65 Å
AuthorsButs, L. / De Genst, E. / Loris, R. / Oscarson, S. / Lahmann, M. / Messens, J. / Brosens, E. / Wyns, L. / Bouckaert, J. / De Greve, H.
Citation
Journal: Mol.Microbiol. / Year: 2003
Title: The Fimbrial Adhesin F17-G of Enterotoxigenic Escherichia Coli Has an Immunoglobulin-Like Lectin Domain that Binds N-Acetylglucosamine
Authors: Buts, L. / Bouckaert, J. / De Genst, E. / Loris, R. / Oscarson, S. / Lahmann, M. / Messens, J. / Brosens, E. / Wyns, L. / De Greve, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Solving the Phase Problem for Carbohydrate -Binding Proteins Using Selenium Derivatives of Their Ligands: A Case Study Involving the Bacterial F17-G Adhesin
Authors: Buts, L. / Loris, R. / De Genst, E. / Oscarson, S. / Lahmann, M. / Messens, J. / Brosens, E. / Wyns, L. / De Greve, H. / Bouckaert, J.
#2: Journal: J.Bacteriol. / Year: 1991
Title: Identification, Characterization and Nucleotide Sequence of the F17G Gene, which Determines Receptor Binding of Escherichia Coli F17 Fimbriae
Authors: Lintermans, P.F. / Bertels, A. / Schlicker, C. / Deboeck, F. / Charlier, G. / Pohl, P. / Norgren, M. / Normark, S. / Van Montagu, M. / De Greve, H.
History
DepositionDec 20, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F17A-G FIMBRIAL ADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2692
Polymers19,0481
Non-polymers2211
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.329, 42.329, 268.714
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 FIMBRIAL ADHESIN / F17-AG LECTIN


Mass: 19048.227 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING DOMAIN, 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 / References: UniProt: Q99003
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.89 Å3/Da / Density % sol: 33 %
Crystal growpH: 4.6
Details: 30% PEG4000, 0.1M SODIUM ACETATE (PH 4.6), 0.2M AMMONIUM ACETATE
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH8.
2150 mM1dropNaCl
330 %PEG40001reservoir
40.1 Msodium acetate1reservoirpH4.6
50.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8019
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8019 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 20396 / % possible obs: 100 % / Redundancy: 48 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.073 / Net I/σ(I): 8.2
Reflection shellResolution: 1.66→1.81 Å / Rsym value: 0.52 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9V

1o9v


Resolution: 1.65→24.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1557043.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1079 5.9 %RANDOM
Rwork0.211 ---
obs0.211 18442 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.5472 Å2 / ksol: 0.395503 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å2-1.13 Å20 Å2
2---2.85 Å20 Å2
3---5.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 15 111 1370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 168 5.6 %
Rwork0.291 2823 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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