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- PDB-1oio: GafD (F17c-type) Fimbrial adhesin from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1oio
TitleGafD (F17c-type) Fimbrial adhesin from Escherichia coli
ComponentsFIMBRIAL LECTIN
KeywordsLECTIN / ADHESIN / N-ACETYL-D-GLUCOSAMINE BINDING / GLCNAC BINDING LECTIN
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
F17g-G fimbrial adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.7 Å
AuthorsMerckel, M.C. / Tanskanen, J. / Edelman, S. / Westerlund-Wikstrom, B. / Korhonen, T.K. / Goldman, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Structural Basis of Receptor-Binding by Escherichia Coli Associated with Diarrhea and Septicemia
Authors: Merckel, M.C. / Tanskanen, J. / Edelman, S. / Westerlund-Wikstrom, B. / Korhonen, T.K. / Goldman, A.
History
DepositionJun 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: FIMBRIAL LECTIN
B: FIMBRIAL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0556
Polymers38,1702
Non-polymers8854
Water4,252236
1
A: FIMBRIAL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5273
Polymers19,0851
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FIMBRIAL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5273
Polymers19,0851
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.990, 70.470, 56.110
Angle α, β, γ (deg.)90.00, 104.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIMBRIAL LECTIN / GAFD


Mass: 19085.053 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 23-200
Source method: isolated from a genetically manipulated source
Details: 2 NAG (GLCNAC) MOLECULES PER MONOMER DISULPHIDE BETWEEN C53 AND C110
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: ETEC STRAINS / Description: RESIDUES 1-178 / Plasmid: PGAFD(1-178) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47341
#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.: 4
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.: 236 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growpH: 7.5
Details: 10% PEG 6000 100 MM HEPES PH 7.5, 5% MPD, 5% GLCNAC
Crystal grow
*PLUS
Temperature: 4. ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG60001reservoir
2100 mMHEPES1reservoirpH7.5
35 %(v/v)MPD1reservoir
410-30 mg/mlprotein1drop
55 %(w/v)GlcNAc1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 15, 2001 / Details: MIRRORS
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 84352 / % possible obs: 88.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 25.3
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.5 / % possible all: 42.8
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 155927
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 42.8 % / Num. unique obs: 2231 / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1159682.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 6186 9.7 %RANDOM
Rwork0.216 ---
obs0.216 63688 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.8953 Å2 / ksol: 0.366044 e/Å3
Displacement parametersBiso mean: 10.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å22.46 Å2
2---0.14 Å20 Å2
3---0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 60 236 2980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 1.7→1.81 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 981 10.1 %
Rwork0.239 8726 -
obs--82.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 500 Å / Num. reflection all: 63688 / Num. reflection obs: 57502
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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