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- PDB-3jwn: Complex of FimC, FimF, FimG and FimH -

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Basic information

Entry
Database: PDB / ID: 3jwn
TitleComplex of FimC, FimF, FimG and FimH
Components
  • Chaperone protein fimC
  • FimH protein
  • Protein fimF
  • Protein fimG
Keywordsprotein binding/cell adhesion / fimbria / cell adhesion / fimh / fimc / fimf / fimg / chaperone / fibrium / immunoglobulin domain / Fimbrium / Periplasm / Disulfide bond / protein binding-cell adhesion COMPLEX
Function / homology
Function and homology information


pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space ...pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / metal ion binding
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / 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 fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
FimH protein / Protein FimF / Protein FimG / Chaperone protein FimC / FimH protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLe Trong, I. / Aprikian, P. / Stenkamp, R.E. / Sokurenko, E.V.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting.
Authors: Le Trong, I. / Aprikian, P. / Kidd, B.A. / Forero-Shelton, M. / Tchesnokova, V. / Rajagopal, P. / Rodriguez, V. / Interlandi, G. / Klevit, R. / Vogel, V. / Stenkamp, R.E. / Sokurenko, E.V. / Thomas, W.E.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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
C: Chaperone protein fimC
E: Protein fimF
F: Protein fimF
G: Protein fimG
H: FimH protein
I: Chaperone protein fimC
K: Protein fimF
L: Protein fimF
M: Protein fimG
N: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,17212
Polymers197,98710
Non-polymers1842
Water50428
1
C: Chaperone protein fimC
E: Protein fimF
F: Protein fimF
G: Protein fimG
H: FimH protein


Theoretical massNumber of molelcules
Total (without water)98,9945
Polymers98,9945
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-42 kcal/mol
Surface area42520 Å2
MethodPISA
2
I: Chaperone protein fimC
K: Protein fimF
L: Protein fimF
M: Protein fimG
N: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1787
Polymers98,9945
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-43.8 kcal/mol
Surface area42070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.025, 216.025, 532.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 4 types, 10 molecules CIEFKLGMHN

#1: Protein Chaperone protein fimC


Mass: 22754.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4316, fimC, JW4279 / Plasmid: PET22B based PTIPKB91 / Production host: Escherichia coli (E. coli) / References: UniProt: P31697
#2: Protein
Protein fimF


Mass: 16161.095 Da / Num. of mol.: 4 / Fragment: UNP residues 23-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4318, fimF, JW4281 / Production host: Escherichia coli (E. coli) / References: UniProt: P08189
#3: Protein Protein fimG


Mass: 14864.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4319, fimG, JW4282 / Production host: Escherichia coli (E. coli) / References: UniProt: P08190
#4: Protein FimH protein


Mass: 29053.260 Da / Num. of mol.: 2 / Fragment: UNP residues 25-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: F18 / Gene: ECP_4655, fimh / Production host: Escherichia coli (E. coli) / References: UniProt: Q0T8Y8, UniProt: A0A0R4I961*PLUS

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Non-polymers , 2 types, 30 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.03 Å3/Da / Density % sol: 79.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 1.6 M potassium chloride, 0.1 M sodium citrate, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2008
RadiationMonochromator: double-crystal, SI(111), liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→176.8 Å / Num. obs: 119926 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 14
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.862 / % possible all: 46.7

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Processing

Software
NameVersionClassification
PHASERphasing
MOLREPphasing
REFMAC5.5.0096refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1KLF, 3BWU and 3BFQ

1klf

3bwu

3bfq


Resolution: 2.69→48.34 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.362 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27208 6018 5 %RANDOM
Rwork0.24364 ---
obs0.24506 113836 90.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.028 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13822 0 12 28 13862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214146
X-RAY DIFFRACTIONr_bond_other_d0.0020.028904
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.95319357
X-RAY DIFFRACTIONr_angle_other_deg0.744321955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43651851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92825.262572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.372152120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2311557
X-RAY DIFFRACTIONr_chiral_restr0.0530.22337
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022646
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_it0.3571.59257
X-RAY DIFFRACTIONr_mcbond_other0.0281.53756
X-RAY DIFFRACTIONr_mcangle_it0.658214994
X-RAY DIFFRACTIONr_scbond_it0.50734889
X-RAY DIFFRACTIONr_scangle_it0.8864.54361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 225 -
Rwork0.405 4023 -
obs--43.68 %

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