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- PDB-5lne: E. coli F9 pilus adhesin FmlH bound to the Thomsen-Friedenreich (... -

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Basic information

Entry
Database: PDB / ID: 5lne
TitleE. coli F9 pilus adhesin FmlH bound to the Thomsen-Friedenreich (TF) antigen
ComponentsPutative Fml fimbrial adhesin FmlD
KeywordsCELL ADHESION / fimbrial adhesin / lectin / O-glycan
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
Thomsen-Friedenreich antigen / NICKEL (II) ION / Hypothetical fimbrial-like protein ydeQ / Putative Fml fimbrial adhesin FmlD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRuer, S. / Conover, M.S. / Kalas, V. / Taganna, J. / De Greve, H. / Pinkner, J.S. / Dodson, K.W. / Hultgren, S.J. / Remaut, H.
Funding support Belgium, United States, 2items
OrganizationGrant numberCountry
FWOG030411N Belgium
National Institutes of HealthDK051406 United States
CitationJournal: Cell Host Microbe / Year: 2016
Title: Inflammation-Induced Adhesin-Receptor Interaction Provides a Fitness Advantage to Uropathogenic E. coli during Chronic Infection.
Authors: Conover, M.S. / Ruer, S. / Taganna, J. / Kalas, V. / De Greve, H. / Pinkner, J.S. / Dodson, K.W. / Remaut, H. / Hultgren, S.J.
History
DepositionAug 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Fml fimbrial adhesin FmlD
B: Putative Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4375
Polymers35,6122
Non-polymers8253
Water1,44180
1
A: Putative Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1892
Polymers17,8061
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2483
Polymers17,8061
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.820, 51.460, 53.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 1 - 156 / Label seq-ID: 1 - 156

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative Fml fimbrial adhesin FmlD / FmlH


Mass: 17805.984 Da / Num. of mol.: 2 / Fragment: UNP residues 25-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fmlD, UTI89_C1716 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q1RBS0, UniProt: A0A0H2V7F6*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Citrate pH2, 2.2M ammonium sulfate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 2.2→59.4 Å / Num. all: 122486 / Num. obs: 17285 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 39.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.8 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.792 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22446 877 5.1 %RANDOM
Rwork0.18014 ---
obs0.18241 16407 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 2.2→59.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 53 80 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192534
X-RAY DIFFRACTIONr_bond_other_d0.0080.022328
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.9483466
X-RAY DIFFRACTIONr_angle_other_deg1.47835354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2415308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.39525104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88615360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.986154
X-RAY DIFFRACTIONr_chiral_restr0.1220.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212838
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02584
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1953.0591250
X-RAY DIFFRACTIONr_mcbond_other2.1943.0571249
X-RAY DIFFRACTIONr_mcangle_it3.4294.5591552
X-RAY DIFFRACTIONr_mcangle_other3.4284.561553
X-RAY DIFFRACTIONr_scbond_it2.8963.3611284
X-RAY DIFFRACTIONr_scbond_other2.8963.3611284
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5364.9271915
X-RAY DIFFRACTIONr_long_range_B_refined6.35224.5512567
X-RAY DIFFRACTIONr_long_range_B_other6.32624.532559
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16436 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 55 -
Rwork0.206 1209 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.55310.0790.15760.13450.08510.3477-0.0130.08180.00330.02640.01480.01330.0060.0243-0.00180.0864-0.00370.00480.01220.00080.0017-14.4275-21.415715.2337
20.2216-0.03650.03340.0253-0.0720.2404-0.003-0.0120.0296-0.00370.0083-0.0017-0.0087-0.0267-0.00540.1014-0.0035-0.00070.0064-0.00430.0091-13.9263-45.829327.5796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 202
2X-RAY DIFFRACTION2B1 - 202

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