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- PDB-7b0w: Crystal structure of the E. coli type 1 pilus assembly inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 7b0w
TitleCrystal structure of the E. coli type 1 pilus assembly inhibitor FimI bound to FimC
Components
  • Chaperone protein FimC
  • Fimbrin-like protein FimI
KeywordsSTRUCTURAL PROTEIN / structural protein complex / pilus assembly
Function / homology
Function and homology information


pilus assembly / cell adhesion involved in single-species biofilm formation / pilus / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space
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 / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Chaperone protein FimC / Fimbrin-like protein FimI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsScharer, M.A. / Zigova, Z. / Giese, C. / Puorger, C. / Ignatov, O. / Capitani, G. / Glockshuber, R.
Funding support1items
OrganizationGrant numberCountry
Swiss National Science Foundation
CitationJournal: To Be Published
Title: Comprehensive kinetic characterization of bacterial pilus rod assembly and assembly termination
Authors: Giese, C. / Puorger, C. / Ignatov, O. / Zigova, Z. / Weber, M. / Scharer, M.A. / Capitani, G. / Glockshuber, R.
History
DepositionNov 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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

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Assembly

Deposited unit
C: Chaperone protein FimC
I: Fimbrin-like protein FimI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,19814
Polymers38,6142
Non-polymers58412
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: the proteins co-elute during ion exchange chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-7 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.220, 166.220, 51.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Chaperone protein FimC


Mass: 23582.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimC, b4316, JW4279 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31697
#2: Protein Fimbrin-like protein FimI


Mass: 15030.870 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimI, b4315, JW5779 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39264
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 4.5 M sodium formate, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→48.44 Å / Num. obs: 81377 / % possible obs: 99.1 % / Redundancy: 3.431 % / Biso Wilson estimate: 30.672 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.086 / Χ2: 0.972 / Net I/σ(I): 11.64 / Num. measured all: 279213 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.83.5251.0871.2621175603960070.5031.27899.5
1.8-1.843.4980.8271.6320612591858930.6310.97499.6
1.84-1.93.4910.6472.1119800569256710.7580.76399.6
1.9-1.963.4770.4832.7319258556155390.8090.5799.6
1.96-2.023.4350.3733.5218298537253270.8790.44299.2
2.02-2.093.3390.2884.3217193519351490.9230.34399.2
2.09-2.173.1290.2185.1815575506049780.9470.26398.4
2.17-2.263.2430.1686.7615528484847880.9690.20198.8
2.26-2.363.3410.1428.0115474465446310.9760.16999.5
2.36-2.473.6220.1369.0616120446744500.9820.1699.6
2.47-2.613.6060.10311.5615214423342190.990.12199.7
2.61-2.773.5650.08613.5114246401339960.9920.10199.6
2.77-2.963.5120.06717.1413146375737430.9950.07999.6
2.96-3.23.4850.04922.2112287355035260.9970.05899.3
3.2-3.53.4320.03727.9910942322331880.9980.04498.9
3.5-3.913.0940.02932.149006296029110.9980.03698.3
3.91-4.523.0490.02536.037745259125400.9990.0398
4.52-5.533.6440.02442.617988223421920.9990.02898.1
5.53-7.833.7010.02839.66281173916970.9990.03397.6
7.83-48.443.5680.02149.1433259909320.9990.02594.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWH

4dwh


Resolution: 1.75→48.44 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 977 1.2 %
Rwork0.1708 80392 -
obs0.171 81369 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 34.5005 Å2 / Biso min: 11.67 Å2
Refinement stepCycle: final / Resolution: 1.75→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 38 441 3076
Biso mean--43.21 40.76 -
Num. residues----341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.840.30321390.2849114711161099
1.84-1.960.24831390.24311143111570100
1.96-2.110.22791390.198114081154799
2.11-2.320.18991390.1789114381157799
2.32-2.660.18511390.17641149111630100
2.66-3.350.20091410.1693115741171599
3.35-48.440.14541410.1358115791172098
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)
12.75621.5192-0.72481.1818-0.2459-0.11950.2925-0.9354-0.25730.3439-0.3642-0.226-0.1960.27880.02690.2835-0.1811-0.07220.53520.04050.2465286.648162.102621.567
21.85970.867-0.01923.23420.32742.1313-0.02420.21510.1768-0.08080.021-0.0122-0.20710.11110.00210.1331-0.04410.00340.23770.00780.1407270.201858.3722.2264
31.09340.3826-0.13181.0597-0.23941.71470.0045-0.0609-0.07240.11280.0321-0.00150.17580.1465-0.03930.12430.0132-0.01060.1592-0.02290.1218264.470542.276217.7517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain II21 - 160
2X-RAY DIFFRACTION2chain C and resi 1:90C1 - 90
3X-RAY DIFFRACTION3chain C and resi 100:205C100 - 205

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