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- PDB-9at9: Crystal structure of Klebsiella pneumoniae FimH lectin domain bou... -

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Basic information

Entry
Database: PDB / ID: 9at9
TitleCrystal structure of Klebsiella pneumoniae FimH lectin domain bound to D-mannose
ComponentsFimH
KeywordsCELL ADHESION / Lectin domain / adhesin / complex / type 1 pilus
Function / homology
Function and homology information


pilus / cell adhesion
Similarity search - Function
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.
Similarity search - Domain/homology
alpha-D-mannopyranose / FimH
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsLopatto, E. / Tamadonfar, K.O. / Hultgren, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI029549 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI048689 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI157797 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Conformational ensembles in Klebsiella pneumoniae FimH impact uropathogenesis.
Authors: Lopatto, E.D.B. / Pinkner, J.S. / Sanick, D.A. / Potter, R.F. / Liu, L.X. / Bazan Villicana, J. / Tamadonfar, K.O. / Ye, Y. / Zimmerman, M.I. / Gualberto, N.C. / Dodson, K.W. / Janetka, J.W. ...Authors: Lopatto, E.D.B. / Pinkner, J.S. / Sanick, D.A. / Potter, R.F. / Liu, L.X. / Bazan Villicana, J. / Tamadonfar, K.O. / Ye, Y. / Zimmerman, M.I. / Gualberto, N.C. / Dodson, K.W. / Janetka, J.W. / Hunstad, D.A. / Hultgren, S.J.
History
DepositionFeb 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9992
Polymers17,8191
Non-polymers1801
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.539, 40.626, 101.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein FimH / Fimbrial protein


Mass: 17818.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: TOP52 1721 / Gene: fimH, fimH_1, fimH_2 / Production host: Escherichia coli (E. coli) / References: UniProt: B0LF88
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: Protein mixed with 10:1 molar ratio of D-mannose to protein. Crystals grown in 0.4 M MgCl2, 2.0 M NaCl, 0.1 M Tris pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072156 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072156 Å / Relative weight: 1
ReflectionResolution: 1.34→35.19 Å / Num. obs: 35168 / % possible obs: 98.92 % / Redundancy: 2 % / Biso Wilson estimate: 14.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03579 / Net I/σ(I): 12.92
Reflection shellResolution: 1.34→1.388 Å / Num. unique obs: 3188 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIXv1.20.1refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→35.19 Å / SU ML: 0.1845 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 1728 4.91 %
Rwork0.2153 33433 -
obs0.2161 35161 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.08 Å2
Refinement stepCycle: LAST / Resolution: 1.34→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 12 86 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871255
X-RAY DIFFRACTIONf_angle_d1.03771730
X-RAY DIFFRACTIONf_chiral_restr0.0831209
X-RAY DIFFRACTIONf_plane_restr0.0087219
X-RAY DIFFRACTIONf_dihedral_angle_d6.1852186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.37551600.36442460X-RAY DIFFRACTION90.2
1.38-1.420.33861250.33192733X-RAY DIFFRACTION98.5
1.42-1.470.32361530.30992712X-RAY DIFFRACTION98.8
1.47-1.530.33231390.27912801X-RAY DIFFRACTION99.9
1.53-1.60.25441510.2472755X-RAY DIFFRACTION100
1.6-1.690.26931650.23782786X-RAY DIFFRACTION99.9
1.69-1.790.25911650.22582791X-RAY DIFFRACTION100
1.79-1.930.252511350.21712817X-RAY DIFFRACTION100
1.93-2.130.19561170.20342857X-RAY DIFFRACTION99.9
2.13-2.430.20571210.20092848X-RAY DIFFRACTION100
2.43-3.070.23711610.21042867X-RAY DIFFRACTION99.9
3.07-35.190.1881540.18333006X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: -8.91365102814 Å / Origin y: 5.29153969459 Å / Origin z: -13.8113654975 Å
111213212223313233
T0.14237435207 Å20.020076723455 Å2-0.00468842694848 Å2-0.131298688257 Å2-0.010918518568 Å2--0.167379994658 Å2
L1.11851821668 °2-0.287502648802 °21.47782591666 °2-0.694849017613 °2-0.143043781329 °2--3.82334017858 °2
S0.0913414318495 Å °0.103489286353 Å °-0.0573270293892 Å °-0.137316607869 Å °-0.0756635272436 Å °0.0435516426906 Å °0.044532905473 Å °0.00191843705122 Å °-0.019539912532 Å °
Refinement TLS groupSelection details: all

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