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- PDB-2bs8: Crystal structure of F17b-G in complex with N-acetyl-D-glucosamine -

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Basic information

Entry
Database: PDB / ID: 2bs8
TitleCrystal structure of F17b-G in complex with N-acetyl-D-glucosamine
ComponentsADHESIN
KeywordsSUGAR BINDING PROTEIN / LECTIN / FIMBRIAE / PROTEIN-SUGAR COMPLEX / SUGAR-BINDING PROTEIN
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
F17b-G fimbrial adhesin
Similarity search - Component
Biological speciesESCHERICHIA COLI B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsButs, L. / Wellens, A. / VanMolle, I. / Wyns, L. / Loris, R. / Lahmann, M. / Oscarson, S. / DeGreve, 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 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 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 1.5Dec 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 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

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Assembly

Deposited unit
A: ADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1182
Polymers18,8971
Non-polymers2211
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.506, 96.506, 97.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein ADHESIN / F17BG


Mass: 18896.871 Da / Num. of mol.: 1 / Fragment: LECTIN DOMAIN, RESIDUES 23-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI B (bacteria) / Description: F17-POSITIVE E. COLI ISOLATE STRAIN / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q47200
#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.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsELECTRON DENSITY AND NUCLEOTIDE SEQUENCING CONFIRMED RESIDUE 110 IN CHAIN A TO BE A CYSTEINE, NOT SERINE.

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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: 3 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP: 1 MICROLITER OF 10% ETHANOL WITH 1.5 M NACL PLUS 1 MICROLITER OF 16 MG/ML F17BG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2002 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.24→23 Å / Num. obs: 11000 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5 / % possible all: 91.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9W

1o9w


Resolution: 2.25→22.91 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2439377.41 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3972 1122 10.3 %RANDOM
Rwork0.3317 ---
obs0.3317 10924 96.8 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 216.269 Å2 / ksol: 0.466888 e/Å3
Displacement parametersBiso mean: 35.35 Å2
Baniso -1Baniso -2Baniso -3
1--6.18 Å20 Å20 Å2
2---6.18 Å20 Å2
3---12.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.25→22.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 15 199 1543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 2.25→2.32 Å / Total num. of bins used: 10 / % reflection obs: 91.1 %

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