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- PDB-6arm: F9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystal... -

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Basic information

Entry
Database: PDB / ID: 6arm
TitleF9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystallized with o-nitrophenyl beta-galactoside (ONPG)
ComponentsF9 pilus adhesin FmlH
KeywordsSUGAR BINDING PROTEIN / Fimbrial adhesin / lectin / bacterial adhesion
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
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
2-nitrophenyl beta-D-galactopyranoside / Putative Fml fimbrial adhesin FmlD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKalas, V. / Hultgren, S.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2018
Title: Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection.
Authors: Kalas, V. / Hibbing, M.E. / Maddirala, A.R. / Chugani, R. / Pinkner, J.S. / Mydock-McGrane, L.K. / Conover, M.S. / Janetka, J.W. / Hultgren, S.J.
History
DepositionAug 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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
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: F9 pilus adhesin FmlH
B: F9 pilus adhesin FmlH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5395
Polymers35,8402
Non-polymers6993
Water5,873326
1
A: F9 pilus adhesin FmlH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3173
Polymers17,9201
Non-polymers3972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F9 pilus adhesin FmlH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2212
Polymers17,9201
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.002, 51.269, 114.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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Components

#1: Protein F9 pilus adhesin FmlH


Mass: 17920.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: fmlD, UTI89_C1716 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1RBS0
#2: Sugar ChemComp-145 / 2-nitrophenyl beta-D-galactopyranoside / 1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE / 2-nitrophenyl beta-D-galactoside / 2-nitrophenyl D-galactoside / 2-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
1-O-[O-nitrophenyl]-b-D-galactopyranoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M ammonium sulfate, 0.1M NaCl, 0.1 M MES pH 5.6, 32% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→57.3 Å / Num. obs: 46203 / % possible obs: 96 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Net I/σ(I): 15.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.365 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1811 / CC1/2: 0.288 / Rpim(I) all: 0.687 / % possible all: 79.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AOW

6aow


Resolution: 1.5→50 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.03
RfactorNum. reflection% reflection
Rfree0.2399 2253 4.89 %
Rwork0.2008 --
obs0.2028 46110 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 47 326 2682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072428
X-RAY DIFFRACTIONf_angle_d1.0933328
X-RAY DIFFRACTIONf_dihedral_angle_d11.322824
X-RAY DIFFRACTIONf_chiral_restr0.041383
X-RAY DIFFRACTIONf_plane_restr0.004420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53270.43471210.35442118X-RAY DIFFRACTION77
1.5327-1.56830.35091180.32832448X-RAY DIFFRACTION86
1.5683-1.60750.31561250.28812541X-RAY DIFFRACTION90
1.6075-1.6510.31311180.25792709X-RAY DIFFRACTION95
1.651-1.69960.271390.24842747X-RAY DIFFRACTION98
1.6996-1.75440.28891280.23722798X-RAY DIFFRACTION98
1.7544-1.81720.28481390.22882789X-RAY DIFFRACTION99
1.8172-1.88990.23361140.22132801X-RAY DIFFRACTION98
1.8899-1.97590.28091450.21192801X-RAY DIFFRACTION98
1.9759-2.08010.2261560.19982820X-RAY DIFFRACTION99
2.0801-2.21040.25711480.19622803X-RAY DIFFRACTION99
2.2104-2.38110.23311550.19442841X-RAY DIFFRACTION99
2.3811-2.62070.22521540.19742841X-RAY DIFFRACTION99
2.6207-2.99990.2391750.18682862X-RAY DIFFRACTION100
2.9999-3.77940.19851530.17052898X-RAY DIFFRACTION100
3.7794-500.22011650.18123040X-RAY DIFFRACTION99

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