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- PDB-1zpl: E. coli F17a-G lectin domain complex with GlcNAc(beta1-O)Me -

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Basic information

Entry
Database: PDB / ID: 1zpl
TitleE. coli F17a-G lectin domain complex with GlcNAc(beta1-O)Me
ComponentsF17a-G
KeywordsCELL ADHESION / FIMBRIAE / LECTINS / BACTERIAL ADHESION / PROTEIN-SUGAR COMPLEX
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
methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside / F17a-G fimbrial adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsButs, L. / Wellens, A. / Van Molle, I. / 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 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 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

Downloads & links

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Assembly

Deposited unit
A: F17a-G
B: F17a-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5674
Polymers38,0962
Non-polymers4702
Water8,881493
1
A: F17a-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2832
Polymers19,0481
Non-polymers2351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F17a-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2832
Polymers19,0481
Non-polymers2351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.805, 42.805, 288.244
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein F17a-G


Mass: 19048.227 Da / Num. of mol.: 2 / Fragment: lectin domain (residues 23-199)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: expression vector with a T7 promotor / Gene: F17G AF022140 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q99003
#2: Sugar ChemComp-MAG / methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside / BETA-METHYL-N-ACETYL-D-GLUCOSAMINE / methyl 2-acetamido-2-deoxy-beta-D-glucoside / methyl 2-acetamido-2-deoxy-D-glucoside / methyl 2-acetamido-2-deoxy-glucoside / Methyl group


Type: D-saccharide / Mass: 235.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H17NO6
IdentifierTypeProgram
DGlcpNAc[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-N-acetyl-b-D-glucopyranoseCOMMON NAMEGMML 1.0
a-methyl-N-acetyl-D-glucosamineIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% (v/v) isopropanol, 20% (w/v) PEG 4000, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2004
RadiationMonochromator: ESRF ID14-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 35422 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.335 / % possible all: 70

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Processing

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

1o9v


Resolution: 1.7→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2544 -random
Rwork0.2077 --
all0.2123 18291 -
obs0.2123 18291 -
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 32 493 3071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.007

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