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- PDB-3gfu: FaeE-FaeG chaperone-major pilin complex of F4 ac 5/95 fimbriae -

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Basic information

Entry
Database: PDB / ID: 3gfu
TitleFaeE-FaeG chaperone-major pilin complex of F4 ac 5/95 fimbriae
Components
  • Chaperone protein faeE
  • FaeG
KeywordsCELL ADHESION / immunoglobulin like fold / Chaperone / Fimbrium / Immunoglobulin domain
Function / homology
Function and homology information


pilus / : / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion
Similarity search - Function
Fimbrial, major/minor subunit / Fimbrial, major and minor subunit / 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 ...Fimbrial, major/minor subunit / Fimbrial, major and minor subunit / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein FaeE / FaeG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 Å
AuthorsVan Molle, I. / Moonens, K. / Garcia-Pino, A. / Buts, L. / Bouckaert, J. / De Greve, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and thermodynamic characterization of pre- and postpolymerization states in the F4 fimbrial subunit FaeG
Authors: Van Molle, I. / Moonens, K. / Garcia-Pino, A. / Buts, L. / De Kerpel, M. / Wyns, L. / Bouckaert, J. / De Greve, H.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.name
Revision 1.4Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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
C: Chaperone protein faeE
D: FaeG
A: Chaperone protein faeE
B: FaeG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,49415
Polymers102,4384
Non-polymers1,05711
Water8,251458
1
C: Chaperone protein faeE
D: FaeG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6997
Polymers51,2192
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-19 kcal/mol
Surface area17980 Å2
MethodPISA
2
A: Chaperone protein faeE
B: FaeG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7958
Polymers51,2192
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-20 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.924, 90.108, 86.544
Angle α, β, γ (deg.)90.000, 114.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chaperone protein faeE


Mass: 24801.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: C1360-79 / Gene: faeE / Plasmid: pEXP45 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P25401
#2: Protein FaeG


Mass: 26417.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 5 to 21 were replaced by 6xHis-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ETEC 5/95 / Gene: faeG / Plasmid: pEXP45 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q6T3W5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.6M (NH4)2SO4, 0.1M Na acetate pH 4.6 , VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.815 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2007
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.99→35 Å / Num. all: 67757 / Num. obs: 67757 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.48
Reflection shellResolution: 2→2.09 Å / Redundancy: 4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 78.6

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GEW

3gew


Resolution: 1.991→28.802 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 34.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 3405 5.04 %
Rwork0.2391 --
obs0.2415 67576 94.2 %
all-67757 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.67 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 29.173 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.831 Å2
2---0.188 Å2-0 Å2
3---0.148 Å2
Refinement stepCycle: LAST / Resolution: 1.991→28.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 55 458 6761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126417
X-RAY DIFFRACTIONf_angle_d1.4048731
X-RAY DIFFRACTIONf_dihedral_angle_d15.9072182
X-RAY DIFFRACTIONf_chiral_restr0.0881020
X-RAY DIFFRACTIONf_plane_restr0.0061117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9907-2.01910.34811140.30491973X-RAY DIFFRACTION70
2.0191-2.04920.32721340.28742513X-RAY DIFFRACTION89
2.0492-2.08120.29391300.28612526X-RAY DIFFRACTION89
2.0812-2.11530.33671310.27582499X-RAY DIFFRACTION90
2.1153-2.15180.35111300.26972560X-RAY DIFFRACTION90
2.1518-2.19090.3081360.28132549X-RAY DIFFRACTION90
2.1909-2.2330.37111520.32582525X-RAY DIFFRACTION91
2.233-2.27860.36021360.32962519X-RAY DIFFRACTION89
2.2786-2.32810.39481250.30042625X-RAY DIFFRACTION92
2.3281-2.38230.29411320.24952622X-RAY DIFFRACTION93
2.3823-2.44180.36561430.24872703X-RAY DIFFRACTION95
2.4418-2.50780.33461380.24532719X-RAY DIFFRACTION96
2.5078-2.58150.27611480.23822734X-RAY DIFFRACTION97
2.5815-2.66480.3041480.24232801X-RAY DIFFRACTION98
2.6648-2.760.2671450.24442781X-RAY DIFFRACTION99
2.76-2.87040.32451610.24552807X-RAY DIFFRACTION99
2.8704-3.00090.30971520.23862825X-RAY DIFFRACTION99
3.0009-3.15890.27631520.22562803X-RAY DIFFRACTION100
3.1589-3.35660.23081460.2262836X-RAY DIFFRACTION99
3.3566-3.61530.28281520.21682821X-RAY DIFFRACTION99
3.6153-3.97820.2251440.20322845X-RAY DIFFRACTION100
3.9782-4.55190.18751500.16652840X-RAY DIFFRACTION99
4.5519-5.72760.20321470.16412887X-RAY DIFFRACTION100
5.7276-28.80470.27621590.21712858X-RAY DIFFRACTION98
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)
10.8840.04280.2587-0.3193-0.00040.3465-0.01630.0434-0.0585-0.0451-0.010.03710.03590.00670.04110.184-0.0140.02350.0214-0.01610.19031.8412-12.9336.7582
21.2235-0.3514-0.0790.5009-0.01670.47580.0713-0.190.01750.0323-0.0243-0.00680.0274-0.057-0.0310.107-0.0150.03040.1281-0.00980.0959-18.3537-10.275221.4658
31.1873-0.1249-0.12890.3833-0.14690.5296-0.0449-0.00510.119-0.02540.013-0.0421-0.0169-0.1420.01260.1043-0.0042-0.00390.2183-0.01820.0779-21.1666-13.1384-20.1002
40.85180.10680.22560.2905-0.0180.74990.02910.05330.1298-0.00560.0015-0.0121-0.02380.0375-0.04720.1126-0.010.01860.19920.00350.1196-0.9613-10.2359-35.0004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 211
2X-RAY DIFFRACTION2chain BB11 - 251
3X-RAY DIFFRACTION3chain CC1 - 212
4X-RAY DIFFRACTION4chain DD10 - 251

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