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- PDB-4y2o: Structure of CFA/I pili chaperone-major subunit complex (CfaA-CfaB) -

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Basic information

Entry
Database: PDB / ID: 4y2o
TitleStructure of CFA/I pili chaperone-major subunit complex (CfaA-CfaB)
Components
  • CFA/I fimbrial subunit B
  • CfA/I fimbrial subunit A (Colonization factor antigen subunit A putative chaperone)
KeywordsSTRUCTURAL PROTEIN / Enterotoxigenic Escherichia coli / periplasmic chaperone / major pilin / self-assembly / fimbriae
Function / homology
Function and homology information


Immunoglobulin-like - #3970 / CFA/I fimbrial subunit E, pilin domain / Fimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / TRIETHYLENE GLYCOL / CfA/I fimbrial subunit A (Colonization factor antigen subunit A putative chaperone) / CFA/I fimbrial subunit B
Similarity search - Component
Biological speciesEscherichia coli O78:H11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.419 Å
AuthorsBao, R. / Xia, D.
CitationJournal: Mol. Microbiol. / Year: 2016
Title: Off-pathway assembly of fimbria subunits is prevented by chaperone CfaA of CFA/I fimbriae from enterotoxigenic E. coli.
Authors: Bao, R. / Liu, Y. / Savarino, S.J. / Xia, D.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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
A: CfA/I fimbrial subunit A (Colonization factor antigen subunit A putative chaperone)
B: CFA/I fimbrial subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6276
Polymers41,2092
Non-polymers4184
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-19 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.192, 129.192, 73.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-340-

HOH

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Components

#1: Protein CfA/I fimbrial subunit A (Colonization factor antigen subunit A putative chaperone)


Mass: 26493.488 Da / Num. of mol.: 1 / Fragment: UNP residues 19-238 / Mutation: T112I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O78:H11 (strain H10407 / ETEC) (bacteria)
Strain: H10407 / ETEC / Gene: cfaA, ETEC_p948_0390 / Production host: Escherichia coli (E. coli) / References: UniProt: E3PPC3
#2: Protein CFA/I fimbrial subunit B / CFA/I antigen / CFA/I pilin / Colonization factor antigen I subunit B


Mass: 14715.560 Da / Num. of mol.: 1 / Fragment: UNP residues 38-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O78:H11 (strain H10407 / ETEC) (bacteria)
Strain: H10407 / ETEC / Gene: cfaB, ETEC_p948_0400 / Production host: Escherichia coli (E. coli) / References: UniProt: E3PPC4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Na2HPO4-NaH2PO4 pH 6.6, 9% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→44.464 Å / Num. obs: 18960 / % possible obs: 96.4 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1 / % possible all: 72.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F84

3f84


Resolution: 2.419→44.464 Å / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 31.2 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2623 881 5.08 %
Rwork0.2356 --
obs0.2368 17344 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.419→44.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 22 139 2894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172803
X-RAY DIFFRACTIONf_angle_d1.3463791
X-RAY DIFFRACTIONf_dihedral_angle_d18.9551039
X-RAY DIFFRACTIONf_chiral_restr0.078440
X-RAY DIFFRACTIONf_plane_restr0.007479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4222-2.57380.31441370.30062700X-RAY DIFFRACTION93
2.5738-2.77230.3111470.27882733X-RAY DIFFRACTION95
2.7723-3.05090.31891390.26742755X-RAY DIFFRACTION95
3.0509-3.49150.25241570.24612739X-RAY DIFFRACTION95
3.4915-4.39550.23051400.21962740X-RAY DIFFRACTION95
4.3955-26.13310.25941570.21532741X-RAY DIFFRACTION95

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