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- PDB-5fwr: Breaking down the wall: mutation of the tyrosine gate of the univ... -

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Basic information

Entry
Database: PDB / ID: 5fwr
TitleBreaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH
ComponentsFimH
KeywordsCELL ADHESION / BACTERIAL ADHESIN / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD
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 / metal ion binding
Similarity search - Function
Fimbrial-type adhesion domain / FimH, mannose-binding domain / FimH, mannose binding / 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 / FimH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsBouckaert, J.
CitationJournal: IUCrJ / Year: 2017
Title: Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding.
Authors: Rabbani, S. / Krammer, E.M. / Roos, G. / Zalewski, A. / Preston, R. / Eid, S. / Zihlmann, P. / Prevost, M. / Lensink, M.F. / Thompson, A. / Ernst, B. / Bouckaert, J.
History
DepositionFeb 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: FimH
B: FimH
C: FimH
D: FimH
E: FimH
F: FimH
G: FimH
H: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,99316
Polymers135,3358
Non-polymers2,6598
Water32,0671780
1
A: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2492
Polymers16,9171
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.015, 74.005, 111.768
Angle α, β, γ (deg.)99.32, 102.97, 97.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FimH


Mass: 16916.828 Da / Num. of mol.: 8 / Fragment: FIMH LECTIN DOMAIN, RESIDUES 22-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9S497, UniProt: P08191*PLUS
#2: Chemical
ChemComp-3X8 / biphenyl-4-yl alpha-D-mannopyranoside


Mass: 332.348 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H20O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1780 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMETHYL 4'-(ALPHA-D-MANNOPYRANOSYLOXY)BIPHENYL-3-CARBOXYLATE (3XB): THE BIPHENYL GROUP STACKS ONTO ...METHYL 4'-(ALPHA-D-MANNOPYRANOSYLOXY)BIPHENYL-3-CARBOXYLATE (3XB): THE BIPHENYL GROUP STACKS ONTO THE CLOSED TYROSINE GATE OF FIMH.

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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: 2.44 Å3/Da / Density % sol: 46.9 % / Description: NONE
Crystal growpH: 7.8
Details: 5% W/V PGA-LM 100 MM TRIS PH 7.8 ; 20% W/V PEG 3350 ; 5 MM 4-BIPHENYL ALPHA-D-MANNOPYRANOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / 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: 2.13→47.63 Å / Num. obs: 85074 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 2.32 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.13
Reflection shellResolution: 2.13→2.26 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.57 / % possible all: 81.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AUU

4auu


Resolution: 2.13→47.627 Å / SU ML: 0.39 / σ(F): 2 / Phase error: 38.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3318 4247 5 %
Rwork0.2248 --
obs0.2303 85006 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→47.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9565 0 192 1780 11537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01510063
X-RAY DIFFRACTIONf_angle_d1.2813849
X-RAY DIFFRACTIONf_dihedral_angle_d12.7255809
X-RAY DIFFRACTIONf_chiral_restr0.0681622
X-RAY DIFFRACTIONf_plane_restr0.0081777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1296-2.15380.3801950.27071790X-RAY DIFFRACTION63
2.1538-2.17920.39961120.26142158X-RAY DIFFRACTION75
2.1792-2.20580.35811210.25222322X-RAY DIFFRACTION82
2.2058-2.23370.3711440.24982719X-RAY DIFFRACTION95
2.2337-2.26310.32211400.24772677X-RAY DIFFRACTION96
2.2631-2.29410.34721480.26032813X-RAY DIFFRACTION96
2.2941-2.32680.3961430.25722718X-RAY DIFFRACTION97
2.3268-2.36160.36551440.25592738X-RAY DIFFRACTION96
2.3616-2.39850.3621460.25312784X-RAY DIFFRACTION97
2.3985-2.43780.38871440.25392725X-RAY DIFFRACTION97
2.4378-2.47980.34991430.24772736X-RAY DIFFRACTION96
2.4798-2.52490.33621470.252800X-RAY DIFFRACTION97
2.5249-2.57350.38391430.25062733X-RAY DIFFRACTION97
2.5735-2.6260.34131470.24582780X-RAY DIFFRACTION97
2.626-2.68310.3771440.24612738X-RAY DIFFRACTION97
2.6831-2.74550.35781480.24622806X-RAY DIFFRACTION98
2.7455-2.81420.36571440.23112734X-RAY DIFFRACTION97
2.8142-2.89020.36841460.2312771X-RAY DIFFRACTION97
2.8902-2.97530.31921470.21972800X-RAY DIFFRACTION97
2.9753-3.07130.32041460.20862767X-RAY DIFFRACTION97
3.0713-3.18110.31861440.20912739X-RAY DIFFRACTION97
3.1811-3.30840.31941470.20192796X-RAY DIFFRACTION97
3.3084-3.45890.29051440.18712730X-RAY DIFFRACTION97
3.4589-3.64120.28371450.19032762X-RAY DIFFRACTION97
3.6412-3.86930.32041490.1932816X-RAY DIFFRACTION97
3.8693-4.16780.31521450.20042758X-RAY DIFFRACTION98
4.1678-4.5870.26871440.18852748X-RAY DIFFRACTION97
4.587-5.250.31171460.19612769X-RAY DIFFRACTION97
5.25-6.61160.34581470.26212788X-RAY DIFFRACTION98
6.6116-47.63860.34531440.27522744X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 21.8366 Å / Origin y: 8.1274 Å / Origin z: -26.6852 Å
111213212223313233
T0.0105 Å2-0.0079 Å20.0058 Å2-0.0206 Å20.0074 Å2--0.0272 Å2
L0.0561 °2-0.0567 °2-0.0305 °2-0.1363 °2-0.002 °2--0.0063 °2
S0.0005 Å °-0.0052 Å °0.0048 Å °0.0133 Å °0.0015 Å °-0.0102 Å °-0.0035 Å °-0.004 Å °-0.0002 Å °
Refinement TLS groupSelection details: ALL

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