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- PDB-4y2l: Structure of CFA/I pili major subunit CfaB trimer -

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Basic information

Entry
Database: PDB / ID: 4y2l
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 / ISOPROPYL ALCOHOL / CFA/I fimbrial subunit B
Function and homology information
Biological speciesEscherichia coli O78:H11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.746 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 2.0Jan 24, 2018Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 2.1Nov 28, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,99012
Polymers95,6696
Non-polymers3216
Water11,440635
1
A: CFA/I fimbrial subunit B
D: CFA/I fimbrial subunit B
E: CFA/I fimbrial subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0156
Polymers47,8353
Non-polymers1803
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-37 kcal/mol
Surface area20020 Å2
MethodPISA
2
B: CFA/I fimbrial subunit B
C: CFA/I fimbrial subunit B
F: CFA/I fimbrial subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9756
Polymers47,8353
Non-polymers1403
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-62 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.266, 105.811, 70.109
Angle α, β, γ (deg.)90.00, 114.05, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 6 / 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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M NaOH-citrate, pH 5.0, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.03319 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.746→40.783 Å / Num. obs: 85281 / % possible obs: 96.4 % / Redundancy: 3.3 % / Net I/σ(I): 8.3
Reflection shellResolution: 1.75→1.82 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.54 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1323)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F84

3f84


Resolution: 1.746→40.783 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 3526 2.36 %Random selection
Rwork0.2036 ---
obs0.2044 149677 84.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.746→40.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6450 0 18 635 7103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156624
X-RAY DIFFRACTIONf_angle_d1.5569062
X-RAY DIFFRACTIONf_dihedral_angle_d15.1882314
X-RAY DIFFRACTIONf_chiral_restr0.0991139
X-RAY DIFFRACTIONf_plane_restr0.0081151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7464-1.77030.378770.36633731X-RAY DIFFRACTION54
1.7703-1.79560.36791370.34444901X-RAY DIFFRACTION71
1.7956-1.82240.35911020.3254969X-RAY DIFFRACTION73
1.8224-1.85090.31351280.32495117X-RAY DIFFRACTION74
1.8509-1.88120.38141290.29765151X-RAY DIFFRACTION75
1.8812-1.91360.33591530.28825356X-RAY DIFFRACTION78
1.9136-1.94840.26161280.25975511X-RAY DIFFRACTION79
1.9484-1.98590.27091290.24475492X-RAY DIFFRACTION80
1.9859-2.02640.25721450.23865584X-RAY DIFFRACTION82
2.0264-2.07050.2671240.235859X-RAY DIFFRACTION83
2.0705-2.11870.25121480.23245774X-RAY DIFFRACTION84
2.1187-2.17160.28231420.21865878X-RAY DIFFRACTION87
2.1716-2.23040.25131340.20956000X-RAY DIFFRACTION86
2.2304-2.2960.24511600.21015958X-RAY DIFFRACTION87
2.296-2.37010.2571290.19956079X-RAY DIFFRACTION88
2.3701-2.45480.27221500.19676125X-RAY DIFFRACTION89
2.4548-2.5530.23051590.19316187X-RAY DIFFRACTION90
2.553-2.66920.19611560.18876289X-RAY DIFFRACTION91
2.6692-2.80990.23531420.18896374X-RAY DIFFRACTION92
2.8099-2.98590.21671640.19276441X-RAY DIFFRACTION93
2.9859-3.21640.22691520.17626568X-RAY DIFFRACTION95
3.2164-3.53990.21451630.17376647X-RAY DIFFRACTION96
3.5399-4.05170.17751660.16276686X-RAY DIFFRACTION97
4.0517-5.10320.18551520.14096751X-RAY DIFFRACTION98
5.1032-40.79430.22491570.19716723X-RAY DIFFRACTION97

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