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- PDB-3f6l: Structure of the F4 fimbrial chaperone FaeE -

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Basic information

Entry
Database: PDB / ID: 3f6l
TitleStructure of the F4 fimbrial chaperone FaeE
ComponentsChaperone protein faeE
KeywordsCHAPERONE / immunoglobulin-like fold / Cell projection / Fimbrium / Immunoglobulin domain / Periplasm / Plasmid
Function / homology
Function and homology information


chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein FaeE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsVan Molle, I. / Moonens, K. / Buts, L. / Garcia-Pino, A. / Wyns, L. / De Greve, H. / Bouckaert, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The F4 fimbrial chaperone FaeE is stable as a monomer that does not require self-capping of its pilin-interactive surfaces
Authors: Van Molle, I. / Moonens, K. / Buts, L. / Garcia-Pino, A. / Panjikar, S. / Wyns, L. / De Greve, H. / Bouckaert, J.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: 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
A: Chaperone protein faeE
B: Chaperone protein faeE


Theoretical massNumber of molelcules
Total (without water)49,6022
Polymers49,6022
Non-polymers00
Water57632
1
A: Chaperone protein faeE


Theoretical massNumber of molelcules
Total (without water)24,8011
Polymers24,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein faeE


Theoretical massNumber of molelcules
Total (without water)24,8011
Polymers24,8011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.730, 78.653, 87.842
Angle α, β, γ (deg.)90.000, 96.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chaperone protein faeE


Mass: 24801.221 Da / Num. of mol.: 2 / Mutation: K15E
Source method: isolated from a genetically manipulated source
Details: araBAD promotor was changed for T7 promotor / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: C1360-79 / Gene: faeE / Plasmid: pHD147 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P25401
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 4.14 Å3/Da / Density % sol: 70.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M tris pH 7.5, 50% MPD, 0.2M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9364 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9364 Å / Relative weight: 1
ReflectionResolution: 2.8→39.3 Å / Num. all: 18291 / Num. obs: 18291 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 54.76 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.91
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7 / Num. unique all: 1794 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3F65

3f65


Resolution: 2.801→29.876 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.733 / SU ML: 0.57 / Isotropic thermal model: isotropic / σ(F): 1.35 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.303 935 5.12 %random 5% of reflections
Rwork0.255 ---
all0.2593 18291 --
obs0.257 18264 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.783 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso max: 199.02 Å2 / Biso mean: 49.259 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1--4.889 Å20 Å2-0.005 Å2
2--2.995 Å2-0 Å2
3---1.894 Å2
Refinement stepCycle: LAST / Resolution: 2.801→29.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 0 32 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033108
X-RAY DIFFRACTIONf_angle_d0.8054243
X-RAY DIFFRACTIONf_chiral_restr0.052500
X-RAY DIFFRACTIONf_plane_restr0.003556
X-RAY DIFFRACTIONf_dihedral_angle_d16.2221090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.801-2.9480.391330.3182386251997
2.948-3.1330.4131200.29824742594100
3.133-3.3740.3421290.27225032632100
3.374-3.7130.3011380.25824612599100
3.713-4.2490.2691360.23224932629100
4.249-5.3490.2441490.2092475262499
5.349-29.8780.2981300.2512537266799
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)
10.2362-0.37930.03771.8727-0.07430.282-0.0240.02330.0587-0.076-0.0381-0.31270.0207-0.0450.04870.32740.00190.08190.3724-0.00430.385713.02218.202239.5764
20.1802-0.2439-0.29060.9713-0.1050.11250.1286-0.0513-0.059-0.2878-0.07760.0810.0815-0.0286-0.03930.61940.0041-0.11780.36360.00840.307-21.945810.81138.8702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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