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- PDB-3f83: Structure of fusion complex of the minor pilin CfaE and major pil... -

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Basic information

Entry
Database: PDB / ID: 3f83
TitleStructure of fusion complex of the minor pilin CfaE and major pilin CfaB of CFA/I pili from ETEC E. coli
ComponentsFusion of the minor pilin CfaE and major pilin CfaB
KeywordsCELL ADHESION / ETEC / E. coli / CFA/I / CfaE / CfaB / Diarrhea / pili / fimbriae / Cell projection / Fimbrium
Function / homology
Function and homology information


CFA/I fimbrial subunit E, adhesin domain / CblD-like pilus biogenesis initiator / CFA/I fimbrial subunit E, adhesin domain / CblD like pilus biogenesis initiator / CFA/I fimbrial subunit E, pilin domain / Fimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CFA/I fimbrial subunit B / CFA/I fimbrial subunit E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXia, D. / Li, Y.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli.
Authors: Li, Y.F. / Poole, S. / Nishio, K. / Jang, K. / Rasulova, F. / McVeigh, A. / Savarino, S.J. / Xia, D. / Bullitt, E.
History
DepositionNov 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion of the minor pilin CfaE and major pilin CfaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6825
Polymers56,3711
Non-polymers3114
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.914, 45.405, 128.473
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fusion of the minor pilin CfaE and major pilin CfaB / Colonization factor antigen I subunit E / CFA/I pilin / Colonization factor antigen I subunit B / ...Colonization factor antigen I subunit E / CFA/I pilin / Colonization factor antigen I subunit B / CFA/I antigen


Mass: 56371.102 Da / Num. of mol.: 1 / Fragment: Fusion of CfaE and CfaB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CfaE,cfaB / Production host: Escherichia coli (E. coli) / References: UniProt: P25734, UniProt: P02971
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growMethod: vapor diffusion / pH: 4
Details: The CfaEB protein was solubilized in a buffer containing 20 mM MES at pH 6.0 plus 100 mM NaCl. Crystallization was done in hanging drop setup of 1ul of protein solution with 1ul of well ...Details: The CfaEB protein was solubilized in a buffer containing 20 mM MES at pH 6.0 plus 100 mM NaCl. Crystallization was done in hanging drop setup of 1ul of protein solution with 1ul of well solution consisting of 10-11% PEG 8000, 200 mM ammonium sulfate, 100 mM citrate at pH 4.0, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.75 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 2.1→49 Å / % possible obs: 92 % / Redundancy: 7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.32 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23438 2273 7.1 %RANDOM
Rwork0.19349 ---
obs0.1965 29552 92.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.651 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å2-1.72 Å2
2--6.06 Å20 Å2
3----3.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 16 192 4064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213941
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9595367
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9553507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1415703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.210.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022937
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.31470
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5435
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.358
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2671.52527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27524093
X-RAY DIFFRACTIONr_scbond_it3.78131414
X-RAY DIFFRACTIONr_scangle_it5.974.51274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 105
Rwork0.226 1588
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)
13.13211.67880.98392.3961.18042.7714-0.14030.5459-0.2344-0.27080.2197-0.07460.10630.024-0.07940.05890.00790.04290.0358-0.02630.0609-9.8032-7.767343.6417
24.98452.14893.40881.85011.75583.2720.07260.2317-0.37260.01880.1033-0.33460.09090.4591-0.17590.05930.01850.03690.16040.00230.129821.511510.748677.2592
32.95330.28050.45142.31061.83437.74370.0160.093-0.04350.0504-0.039-0.0541-0.1192-0.06860.0230.2056-0.0539-0.05650.20710.00930.201641.976931.0642119.0622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 2012 - 179
2X-RAY DIFFRACTION2AA202 - 376180 - 354
3X-RAY DIFFRACTION3AA377 - 529355 - 507

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