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- PDB-7b0x: Crystal structure of the ternary complex of the E. coli type 1 pi... -

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Basic information

Entry
Database: PDB / ID: 7b0x
TitleCrystal structure of the ternary complex of the E. coli type 1 pilus proteins FimC, FimI and the N-terminal domain of FimD
Components
  • Chaperone protein FimC
  • Fimbrin-like protein FimI
  • Outer membrane usher protein FimD
KeywordsSTRUCTURAL PROTEIN / structural protein complex / pilus assembly
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell adhesion involved in single-species biofilm formation / pilus / chaperone-mediated protein folding / protein folding chaperone / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. ...Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal 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 / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer membrane usher protein FimD / Chaperone protein FimC / Fimbrin-like protein FimI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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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
D: Outer membrane usher protein FimD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3404
Polymers52,2783
Non-polymers621
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-17 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.240, 104.160, 132.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Protein Outer membrane usher protein FimD


Mass: 13664.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimD, b4317, JW5780 / Cell line (production host): HM125 / Production host: Escherichia coli (E. coli) / References: UniProt: P30130
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes pH 8.4, 15 % PEG 4000

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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: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.454 Å / Num. obs: 54167 / % possible obs: 99.1 % / Redundancy: 4.185 % / Biso Wilson estimate: 22.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.093 / Χ2: 0.972 / Net I/σ(I): 11.88 / Num. measured all: 226688 / Scaling rejects: 1236
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
1.7-1.744.2111.2581.0516718398639700.4491.44199.6
1.74-1.794.2091.0241.316208386838510.5811.17299.6
1.79-1.844.2610.8311.616142379237880.6660.9599.9
1.84-1.94.1970.921.4415062365135890.7651.05498.3
1.9-1.964.0610.463.3714327359935280.860.5398
1.96-2.034.1460.3733.514191342734230.9110.42799.9
2.03-2.113.9320.2864.6812923331532870.930.33199.2
2.11-2.194.0370.2375.3912911324731980.960.27398.5
2.19-2.294.1470.2396.5612011306628960.960.27594.5
2.29-2.44.350.1747.7712797295629420.9790.19899.5
2.4-2.534.2690.12310.6812102283528350.9880.141100
2.53-2.693.9520.09313.3910602268626830.9920.10799.9
2.69-2.874.4850.07218.0611217250125010.9960.082100
2.87-3.14.570.05623.2510708234423430.9970.063100
3.1-3.44.4630.04229.479739218321820.9980.047100
3.4-3.84.2230.03733.498375200219830.9980.04399.1
3.8-4.394.1710.02940.687370178017670.9990.03399.3
4.39-5.383.7740.02244.825604149614850.9990.02699.3
5.38-7.64.2840.024455167120912060.9990.02799.8
7.6-48.4543.5410.01950.0225147207100.9990.02298.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B0W

7b0w


Resolution: 1.7→48.454 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1083 2 %
Rwork0.2045 53034 -
obs0.2054 54117 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.58 Å2 / Biso mean: 35.01 Å2 / Biso min: 14.58 Å2
Refinement stepCycle: final / Resolution: 1.7→48.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 4 418 4018
Biso mean--51.8 37.61 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073746
X-RAY DIFFRACTIONf_angle_d1.0325101
X-RAY DIFFRACTIONf_chiral_restr0.041581
X-RAY DIFFRACTIONf_plane_restr0.005678
X-RAY DIFFRACTIONf_dihedral_angle_d12.8621391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.77740.36051340.3004656499
1.7774-1.87110.31121340.27556577100
1.8711-1.98830.3951310.3208641397
1.9883-2.14180.26661340.225656599
2.1418-2.35740.36581330.2727649297
2.3574-2.69850.24481360.19836674100
2.6985-3.39970.21571370.19146740100
3.3997-48.4540.20111440.1547700999
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)
10.91990.07380.06351.2808-0.26492.19490.0554-0.08390.03370.1202-0.0545-0.0816-0.02090.0282-0.00120.0875-0.0142-0.01080.1297-0.0050.16665.8989-7.60437.708
21.30560.5310.03246.3978-2.37942.0677-0.02830.00090.2420.46150.0366-0.0362-0.4333-0.0231-0.00320.23190.03870.00040.1985-0.02320.2212-0.921414.1227-3.5497
31.182-1.4034-0.29662.8681.52671.96310.17870.14640.1387-0.5781-0.1098-0.2987-0.26420.0431-0.05650.22250.00060.05330.19820.02080.1649.5503-19.4511-25.9978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain CC1 - 211
2X-RAY DIFFRACTION2chain II21 - 160
3X-RAY DIFFRACTION3chain DD1 - 123

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