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- PDB-7szo: Structure of a bacterial fimbrial tip containing FocH -

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Basic information

Entry
Database: PDB / ID: 7szo
TitleStructure of a bacterial fimbrial tip containing FocH
Components
  • Chaperone protein FimC
  • FimF protein
  • FimG
  • FimH,F1C putative fimbrial adhesin fusion
KeywordsCELL ADHESION / FIMBRIA / FOCH
Function / homology
Function and homology information


pilus / chaperone-mediated protein folding / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion
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 / FimH, mannose-binding domain ...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 protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
FimF protein / FimG / F1C putative fimbrial adhesin / Chaperone protein FimC / FimH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStenkamp, R.E. / Le Trong, I. / Aprikian, P. / Sokurenko, E.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Recombinant FimH Adhesin Demonstrates How the Allosteric Catch Bond Mechanism Can Support Fast and Strong Bacterial Attachment in the Absence of Shear.
Authors: Thomas, W.E. / Carlucci, L. / Yakovenko, O. / Interlandi, G. / Le Trong, I. / Aprikian, P. / Magala, P. / Larson, L. / Sledneva, Y. / Tchesnokova, V. / Stenkamp, R.E. / Sokurenko, E.V.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 31, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Chaperone protein FimC
E: FimF protein
F: FimF protein
G: FimG
H: FimH,F1C putative fimbrial adhesin fusion
I: Chaperone protein FimC
K: FimF protein
L: FimF protein
M: FimG
N: FimH,F1C putative fimbrial adhesin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,09512
Polymers197,91110
Non-polymers1842
Water63135
1
C: Chaperone protein FimC
E: FimF protein
F: FimF protein
G: FimG
H: FimH,F1C putative fimbrial adhesin fusion


Theoretical massNumber of molelcules
Total (without water)98,9565
Polymers98,9565
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-42 kcal/mol
Surface area42360 Å2
MethodPISA
2
I: Chaperone protein FimC
K: FimF protein
L: FimF protein
M: FimG
N: FimH,F1C putative fimbrial adhesin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1407
Polymers98,9565
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-45 kcal/mol
Surface area42020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.777, 214.777, 532.051
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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) / Gene: fimC / Production host: Escherichia coli (E. coli) / References: UniProt: P31697
#2: Protein
FimF protein / Protein FimF / Type 1 fimbria minor subunit FimF / Type 1 fimbriae minor subunit FimF


Mass: 16161.095 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimF, fimF_1, fimF_2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M0WRP3
#3: 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) / Gene: fimG / Production host: Escherichia coli (E. coli) / References: UniProt: A8HPB0
#4: Protein FimH,F1C putative fimbrial adhesin fusion / FimH protein / Fimbrial protein / Minor component of type 1 fimbriae / Protein FimH / Type 1 ...FimH protein / Fimbrial protein / Minor component of type 1 fimbriae / Protein FimH / Type 1 fimbria D-mannose specific adhesin FimH / Type 1 fimbrial adhesin / Type 1 fimbrial adhesin subunit FimH


Mass: 29015.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: fimH, fimH_1, fimH_2, A5U30_000851, AZZ83_003042, BMR21_18285, BON83_01475, BvCmsSIP024_00413, CY655_27460, DS966_19870, eco0007, ELT29_21175, ELT33_17165, EQO00_22790, EWK56_20550, F9B07_ ...Gene: fimH, fimH_1, fimH_2, A5U30_000851, AZZ83_003042, BMR21_18285, BON83_01475, BvCmsSIP024_00413, CY655_27460, DS966_19870, eco0007, ELT29_21175, ELT33_17165, EQO00_22790, EWK56_20550, F9B07_23010, GF147_14570, HL563_18710, NCTC9075_05909, NCTC9434_02335, focH
Production host: Escherichia coli (E. coli) / References: UniProt: Q9F6Z7, UniProt: A8KI79

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Non-polymers , 2 types, 37 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 5.97 Å3/Da / Density % sol: 79.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6 M POTASSIUM CHLORIDE, 0.1 M REMARK 280 SODIUM CITRATE, PH 4.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→176.78 Å / Num. obs: 109868 / % possible obs: 94.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.139 / Χ2: 1.103 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.8-2.930.76998040.956185
2.9-3.023.70.699106080.975192.2
3.02-3.154.10.528110701.05195.7
3.15-3.324.20.364111731.226196.6
3.32-3.534.20.25111671.384196.5
3.53-3.84.30.196111081.242195.7
3.8-4.184.40.149110521.106195.2
4.18-4.794.50.115112820.982196.7
4.79-6.034.60.095111890.956195.5
6.03-176.784.40.058114151.084194.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
REFMAC5.5.0047refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 3jwn

3jwn


Resolution: 2.8→176.78 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.891 / SU B: 13.123 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 5492 5 %RANDOM
Rwork0.2449 ---
obs0.2464 104359 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.6 Å2 / Biso mean: 46.64 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å21.67 Å20 Å2
2--3.35 Å20 Å2
3----5.02 Å2
Refinement stepCycle: final / Resolution: 2.8→176.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13803 0 12 35 13850
Biso mean--49.86 24.92 -
Num. residues----1858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214121
X-RAY DIFFRACTIONr_bond_other_d0.0010.028905
X-RAY DIFFRACTIONr_angle_refined_deg0.911.95219343
X-RAY DIFFRACTIONr_angle_other_deg0.7543.00221933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44251850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17725.297572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82152118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6091558
X-RAY DIFFRACTIONr_chiral_restr0.0550.22340
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022633
LS refinement shellResolution: 2.8→2.869 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.408 352 -
Rwork0.402 6732 -
obs--82.91 %

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