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- PDB-4buq: Crystal structure of wild type FimH lectin domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 4buq
TitleCrystal structure of wild type FimH lectin domain in complex with heptyl alpha-D-mannopyrannoside
ComponentsFIMH
KeywordsCELL ADHESION / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


pilus / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI UTI89 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsRabbani, S. / Bouckaert, J. / Zalewski, A. / Preston, R. / Eid, S. / Thompson, A. / Puorger, C. / Glockshuber, R. / Ernst, B.
CitationJournal: Acs Med.Chem.Lett. / Year: 2013
Title: Validation of Reactivity Descriptors to Assess the Aromatic Stacking within the Tyrosine Gate of Fimh
Authors: Roos, G. / Wellens, A. / Touaibia, M. / Yamakawa, N. / Geerlings, P. / Roy, R. / Wyns, L. / Bouckaert, J.
History
DepositionJun 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / 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 / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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: FIMH
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3904
Polymers33,8342
Non-polymers5572
Water4,702261
1
A: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1952
Polymers16,9171
Non-polymers2781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIMH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1952
Polymers16,9171
Non-polymers2781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.305, 68.070, 95.607
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.: 2 / Fragment: LECTIN DOMAIN, RESIDUES 10-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI UTI89 (bacteria) / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68
#2: Sugar ChemComp-KGM / heptyl alpha-D-mannopyranoside / Heptyl Alpha-D-mannopyrannoside / heptyl alpha-D-mannoside / heptyl D-mannoside / heptyl mannoside


Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26O6 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.89 Å3/Da / Density % sol: 57.4 % / Description: NONE
Crystal growpH: 7.8
Details: 5% PGA-LM, 0.1M TRIS-HCL PH 7.8, 30% V/V PEG 550 MME, 10 MM HEPTYL ALPHA-D-MANNOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. obs: 20238 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 7.24 % / Biso Wilson estimate: 25.87 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.33
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 6.55 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.77 / % possible all: 90.8

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Processing

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

4auu


Resolution: 2.199→45.139 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 31.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 1005 5 %
Rwork0.202 --
obs0.2047 20122 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.2 Å2
Refinement stepCycle: LAST / Resolution: 2.199→45.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 38 261 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082504
X-RAY DIFFRACTIONf_angle_d1.0983441
X-RAY DIFFRACTIONf_dihedral_angle_d12.022879
X-RAY DIFFRACTIONf_chiral_restr0.068407
X-RAY DIFFRACTIONf_plane_restr0.006441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1987-2.31470.32341270.25112443X-RAY DIFFRACTION89
2.3147-2.45970.32461430.23392716X-RAY DIFFRACTION99
2.4597-2.64960.28991440.21982718X-RAY DIFFRACTION99
2.6496-2.91620.26821440.20272746X-RAY DIFFRACTION99
2.9162-3.3380.24131450.19132762X-RAY DIFFRACTION99
3.338-4.20510.24851480.17322811X-RAY DIFFRACTION100
4.2051-45.14840.21931540.20382921X-RAY DIFFRACTION99

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