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- PDB-1zk5: Escherichia coli F17fG lectin domain complex with N-acetylglucosamine -

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Basic information

Entry
Database: PDB / ID: 1zk5
TitleEscherichia coli F17fG lectin domain complex with N-acetylglucosamine
ComponentsF17G adhesin subunit
KeywordsCELL ADHESION / lectin / beta sandwich / protein-structure complex / immunoglobulin-like fold
Function / homology
Function and homology information


adhesion of symbiont to host / pilus / carbohydrate binding / cell adhesion
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
F17f-G fimbrial adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsButs, L. / Wellens, A. / Van Molle, I. / De Genst, E. / Wyns, L. / Loris, R. / Lahmann, M. / Oscarson, S. / De Greve, H. / Bouckaert, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Impact of natural variation in bacterial F17G adhesins on crystallization behaviour.
Authors: Buts, L. / Wellens, A. / Van Molle, I. / Wyns, L. / Loris, R. / Lahmann, M. / Oscarson, S. / De Greve, H. / Bouckaert, J.
History
DepositionMay 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F17G adhesin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0812
Polymers18,8601
Non-polymers2211
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.715, 41.959, 53.422
Angle α, β, γ (deg.)90.0, 97.542, 90.0
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

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Components

#1: Protein F17G adhesin subunit


Mass: 18859.789 Da / Num. of mol.: 1 / Fragment: residues 23-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: 377F17G / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q9RH91
#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 / N-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% (v/v) isopropanol, 20% PEG 4000, 100 mM Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2004
RadiationMonochromator: DESY X11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 33091 / Num. obs: 32992 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.7
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.242 / % possible all: 99

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Processing

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

1o9v


Resolution: 1.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2013 3160 random
Rwork0.1854 --
all0.187 32061 -
obs0.187 31530 -
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 15 229 1527
LS refinement shellResolution: 1.4→1.47 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.249 3392 -
Rwork0.218 --
obs-3754 95.1 %

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