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- PDB-4x50: Crystal structure of FimH in complex with biphenyl alpha-D-mannop... -

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Basic information

Entry
Database: PDB / ID: 4x50
TitleCrystal structure of FimH in complex with biphenyl alpha-D-mannopyranoside
ComponentsProtein FimH
KeywordsSUGAR BINDING PROTEIN / Bacterial Adhesin / Pilus / UPEC / Antagonist Complex
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
biphenyl-4-yl alpha-D-mannopyranoside / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPreston, R.C. / Jakob, R.P. / Fiege, B. / Zihlmann, P. / Rabbani, S. / Schwardt, O. / Jiang, X. / Ernst, B. / Maier, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_144183/1 Switzerland
CitationJournal: Chembiochem / Year: 2015
Title: The Tyrosine Gate of the Bacterial Lectin FimH: A Conformational Analysis by NMR Spectroscopy and X-ray Crystallography.
Authors: Fiege, B. / Rabbani, S. / Preston, R.C. / Jakob, R.P. / Zihlmann, P. / Schwardt, O. / Jiang, X. / Maier, T. / Ernst, B.
History
DepositionDec 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Protein FimH
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8394
Polymers34,1742
Non-polymers6652
Water9,332518
1
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4192
Polymers17,0871
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4192
Polymers17,0871
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.320, 69.290, 95.920
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 Protein FimH


Mass: 17087.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Variant (production host): HM125 / References: UniProt: P08191
#2: Chemical ChemComp-3X8 / biphenyl-4-yl alpha-D-mannopyranoside


Mass: 332.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 19% PEG 8000, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→24.69 Å / Num. obs: 27054 / % possible obs: 92.7 % / Redundancy: 2.1 % / Biso Wilson estimate: 13.27 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.04 Å / Redundancy: 2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1779)refinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWF

1uwf


Resolution: 2→24.688 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 2527 4.97 %Random selection
Rwork0.1745 ---
obs0.1759 50818 92.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.8 Å2
Refinement stepCycle: LAST / Resolution: 2→24.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 48 518 2958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032514
X-RAY DIFFRACTIONf_angle_d1.0283457
X-RAY DIFFRACTIONf_dihedral_angle_d11.206905
X-RAY DIFFRACTIONf_chiral_restr0.036406
X-RAY DIFFRACTIONf_plane_restr0.003444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03850.25441430.24182906X-RAY DIFFRACTION98
2.0385-2.08010.31040.25042122X-RAY DIFFRACTION99
2.0801-2.12530.27491160.2112490X-RAY DIFFRACTION100
2.1253-2.17470.21181520.19382904X-RAY DIFFRACTION100
2.1747-2.2290.21151560.19142869X-RAY DIFFRACTION100
2.229-2.28930.3446680.30371634X-RAY DIFFRACTION56
2.2893-2.35662012858X-RAY DIFFRACTION100
2.3566-2.43260.24961430.1812889X-RAY DIFFRACTION100
2.4326-2.51940.20721340.17332924X-RAY DIFFRACTION99
2.5194-2.62020.19881750.17732820X-RAY DIFFRACTION99
2.6202-2.73930.23081380.16512412X-RAY DIFFRACTION83
2.7393-2.88351552929X-RAY DIFFRACTION100
2.8835-3.06390.19881390.16052877X-RAY DIFFRACTION100
3.0639-3.29990.24731200.16052947X-RAY DIFFRACTION100
3.2999-3.63110.21611340.16622570X-RAY DIFFRACTION89
3.6311-4.15440.18851380.17562360X-RAY DIFFRACTION82
4.1544-5.22591532912X-RAY DIFFRACTION100
5.2259-100.17511580.1542868X-RAY DIFFRACTION99

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