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- PDB-4y2n: Structure of CFA/I pili major subunit CfaB trimer -

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Basic information

Entry
Database: PDB / ID: 4y2n
TitleStructure of CFA/I pili major subunit CfaB trimer
ComponentsCFA/I fimbrial subunit B
KeywordsSTRUCTURAL PROTEIN / Enterotoxigenic Escherichia coli / periplasmic chaperone / major pilin / self-assembly / fimbriae
Function / homologyCFA/I fimbrial subunit E, pilin domain / Fimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / CFA/I fimbrial subunit B
Function and homology information
Biological speciesEscherichia coli O78:H11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CFA/I fimbrial subunit B
A: CFA/I fimbrial subunit B
C: CFA/I fimbrial subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9707
Polymers47,8353
Non-polymers1354
Water2,882160
1
B: CFA/I fimbrial subunit B
A: CFA/I fimbrial subunit B
hetero molecules

B: CFA/I fimbrial subunit B
A: CFA/I fimbrial subunit B
hetero molecules

B: CFA/I fimbrial subunit B
A: CFA/I fimbrial subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,07418
Polymers95,6696
Non-polymers40512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area20650 Å2
ΔGint-101 kcal/mol
Surface area36990 Å2
MethodPISA
2
C: CFA/I fimbrial subunit B
x 6


Theoretical massNumber of molelcules
Total (without water)95,6696
Polymers95,6696
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_645y+1,x-1,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
Buried area19130 Å2
ΔGint-104 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.723, 114.723, 67.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-204-

MG

21A-233-

HOH

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Components

#1: Protein CFA/I fimbrial subunit B / CFA/I antigen / CFA/I pilin / Colonization factor antigen I subunit B


Mass: 15944.916 Da / Num. of mol.: 3 / Fragment: UNP residues 25-170
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 0.2 M MgCl2, 3% ethanol glycol, 16.8% 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: 2.4→29.696 Å / Num. obs: 19692 / % possible obs: 97.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.02 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1323)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F48

3f48


Resolution: 2.4→29.696 Å / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 35.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2603 2022 10.27 %
Rwork0.2373 --
obs0.2396 19692 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 7 160 3370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133257
X-RAY DIFFRACTIONf_angle_d1.5554451
X-RAY DIFFRACTIONf_dihedral_angle_d15.9241138
X-RAY DIFFRACTIONf_chiral_restr0.095563
X-RAY DIFFRACTIONf_plane_restr0.009563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4009-2.46090.35431340.32961199X-RAY DIFFRACTION83
2.4609-2.52740.35491350.31921188X-RAY DIFFRACTION84
2.5274-2.60170.3271340.28891233X-RAY DIFFRACTION86
2.6017-2.68550.33221370.28971213X-RAY DIFFRACTION86
2.6855-2.78140.29971350.26231225X-RAY DIFFRACTION86
2.7814-2.89260.30391390.26331244X-RAY DIFFRACTION87
2.8926-3.02410.27051430.25121237X-RAY DIFFRACTION87
3.0241-3.18320.26071430.24281279X-RAY DIFFRACTION89
3.1832-3.38220.27951400.22981281X-RAY DIFFRACTION89
3.3822-3.64260.31171420.23011275X-RAY DIFFRACTION90
3.6426-4.00780.2481480.22661307X-RAY DIFFRACTION90
4.0078-4.58470.21791490.20261306X-RAY DIFFRACTION90
4.5847-5.76450.19721450.20011323X-RAY DIFFRACTION90
5.7645-25.01650.23621490.23741382X-RAY DIFFRACTION90

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