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- PDB-5aap: Complex of the FimH lectin with a C-linked para-biphenyl methylen... -

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Basic information

Entry
Database: PDB / ID: 5aap
TitleComplex of the FimH lectin with a C-linked para-biphenyl methylene alpha-D-mannoside
ComponentsFIMH
KeywordsCELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / cell adhesion
Similarity search - Function
Fimbrial-type adhesion domain / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like ...Fimbrial-type adhesion domain / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PARA-BIPHENYL METHYLENE C-LINKED MANNOSIDE / FimH / Type 1 fimbiral adhesin FimH
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.302 Å
AuthorsDe Ruyck, J. / Bouckaert, J.
CitationJournal: Iucrj / Year: 2016
Title: Structures of C-Mannosylated Anti-Adhesives Bound to the Type 1 Fimbrial Fimh Adhesin
Authors: De Ruyck, J. / Lensink, M.F. / Bouckaert, J.
History
DepositionJul 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Structure summary
Revision 1.2May 18, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4274
Polymers16,9171
Non-polymers5113
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.180, 41.710, 97.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FIMH


Mass: 16916.828 Da / Num. of mol.: 1 / Fragment: LECTIN DOMAIN, UNP RESIDUES 10-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68, UniProt: Q1R2J4*PLUS
#2: Chemical ChemComp-VNY / PARA-BIPHENYL METHYLENE C-LINKED MANNOSIDE


Mass: 356.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 1.87 Å3/Da / Density % sol: 34.2 % / Description: NONE
Crystal growpH: 8.6
Details: 30% (V/V) 2-PROPANOL, 100 MM TRIS-HCL PH 8.5, 200 MM AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→41 Å / Num. obs: 26776 / % possible obs: 82.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 6.58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.91
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.85 / % possible all: 39

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AUU

4auu


Resolution: 1.302→38.331 Å / SU ML: 0.08 / σ(F): 2.01 / Phase error: 13.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1501 1339 5 %
Rwork0.122 --
obs0.1234 26776 84.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.4 Å2
Refinement stepCycle: LAST / Resolution: 1.302→38.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 36 271 1503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081327
X-RAY DIFFRACTIONf_angle_d1.4231834
X-RAY DIFFRACTIONf_dihedral_angle_d13.236470
X-RAY DIFFRACTIONf_chiral_restr0.072217
X-RAY DIFFRACTIONf_plane_restr0.007236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3024-1.3490.1769610.14261143X-RAY DIFFRACTION39
1.349-1.4030.1915820.14271561X-RAY DIFFRACTION53
1.403-1.46690.17741170.13712232X-RAY DIFFRACTION75
1.4669-1.54420.1631490.132820X-RAY DIFFRACTION94
1.5442-1.6410.15061500.12832846X-RAY DIFFRACTION95
1.641-1.76770.14181490.1242851X-RAY DIFFRACTION95
1.7677-1.94550.15841530.11952913X-RAY DIFFRACTION96
1.9455-2.2270.14421550.11242933X-RAY DIFFRACTION97
2.227-2.80570.13481570.12182985X-RAY DIFFRACTION97
2.8057-38.34720.14781660.11733153X-RAY DIFFRACTION98

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