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- PDB-3f6i: Structure of the SeMet labeled F4 fibrial chaperone FaeE -

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Basic information

Entry
Database: PDB / ID: 3f6i
TitleStructure of the SeMet labeled F4 fibrial 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 / MAD / Resolution: 2.788 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 / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)49,9782
Polymers49,9782
Non-polymers00
Water23413
1
A: Chaperone protein faeE


Theoretical massNumber of molelcules
Total (without water)24,9891
Polymers24,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein faeE


Theoretical massNumber of molelcules
Total (without water)24,9891
Polymers24,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.285, 75.656, 69.282
Angle α, β, γ (deg.)90.000, 92.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chaperone protein faeE /


Mass: 24988.801 Da / Num. of mol.: 2 / Fragment: UNP residues 35-239 / Mutation: K15E
Source method: isolated from a genetically manipulated source
Details: araBAD promotor was exchanged for T7 promotor / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: C1360-79 / Gene: faeE / Plasmid: pHD163 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P25401
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.87 Å3/Da / Density % sol: 68.21 %
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: 0.9789, 0.9796, 0.9364
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97961
30.93641
ReflectionResolution: 2.7→33 Å / Num. all: 19389 / Num. obs: 19389 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 68.83 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.97
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1890 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.788→31.473 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.752 / SU ML: 0.48 / Isotropic thermal model: isotropic / σ(F): 0.06 / σ(I): 0 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.296 876 5.12 %random 5% of reflections
Rwork0.231 ---
all0.235 17123 --
obs0.23425 17123 96.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.783 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 439.44 Å2 / Biso mean: 65.493 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.052 Å20 Å20.477 Å2
2--1.429 Å20 Å2
3----1.481 Å2
Refinement stepCycle: LAST / Resolution: 2.788→31.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 0 13 2812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052858
X-RAY DIFFRACTIONf_angle_d1.0163906
X-RAY DIFFRACTIONf_chiral_restr0.068469
X-RAY DIFFRACTIONf_plane_restr0.004508
X-RAY DIFFRACTIONf_dihedral_angle_d18.463972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.788-2.9630.3791520.2832533268592
2.963-3.1910.3191300.2562708283897
3.191-3.5120.3321440.232759290398
3.512-4.020.2811330.2182760289399
4.02-5.0610.2321690.1832745291498
5.061-31.4750.3121480.2372742289096
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)
11.1498-0.2751-0.41630.7620.32070.66810.2212-0.0468-0.00770.0701-0.1584-0.19960.05360.0117-0.06330.24850.00450.02260.2263-0.00090.320126.92726.67826.4812
23.02630.2187-0.61230.2809-0.11690.199-0.77340.82990.1737-0.21840.59260.060.2916-0.33390.14320.4486-0.243-0.04670.47840.03250.2832-13.81677.0124.4305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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