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- PDB-3gew: FaeE-FaeG chaperone-major pilin complex of F4 ad fimbriae -

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Basic information

Entry
Database: PDB / ID: 3gew
TitleFaeE-FaeG chaperone-major pilin complex of F4 ad fimbriae
Components
  • Chaperone protein faeE
  • K88 fimbrial protein AD
KeywordsCELL ADHESION / immunoglobulin like fold / Fimbrium / Chaperone / Immunoglobulin domain
Function / homology
Function and homology information


pilus / 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
K88 fimbrial protein AD / Chaperone protein FaeE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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
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
B: Chaperone protein faeE
C: Chaperone protein faeE
D: K88 fimbrial protein AD
A: K88 fimbrial protein AD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,31318
Polymers102,9764
Non-polymers1,33714
Water5,386299
1
B: Chaperone protein faeE
A: K88 fimbrial protein AD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1579
Polymers51,4882
Non-polymers6687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-17 kcal/mol
Surface area17670 Å2
MethodPISA
2
C: Chaperone protein faeE
D: K88 fimbrial protein AD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1579
Polymers51,4882
Non-polymers6687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-16 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.576, 89.757, 85.826
Angle α, β, γ (deg.)90.00, 113.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chaperone protein faeE / 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: pEXP55 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P25401
#2: Protein K88 fimbrial protein AD / FaeGntd / K88 pilin / K88 antigen


Mass: 26686.764 Da / Num. of mol.: 2 / Fragment: FaeGntd
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: C1360-79 / Gene: faeG / Plasmid: pEXP55 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P14191
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICT BASED ON REFERENCE 2 OF DATABASE FAEG3_ECOLX (UNIPROTKB/SWISS-PROT P14191). N27S (UNP ...THE CONFLICT BASED ON REFERENCE 2 OF DATABASE FAEG3_ECOLX (UNIPROTKB/SWISS-PROT P14191). N27S (UNP RESIDUE 59) IS CONFLICT OF FAEG3_ECOLX.

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 283 K / pH: 4.6
Details: 2M (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: 0.95369
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 68837 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 28.62 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.91
Reflection shellResolution: 2→2.09 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.98 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F65 AND 2J6G

3f65

2j6g


Resolution: 2→17.89 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.36 / Phase error: 31.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 3478 5.06 %
Rwork0.223 --
obs0.225 68789 99.2 %
all-68837 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.7 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 33.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.674 Å2-0 Å20.324 Å2
2---1.342 Å2-0 Å2
3---0.669 Å2
Refinement stepCycle: LAST / Resolution: 2→17.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 72 299 6440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086239
X-RAY DIFFRACTIONf_angle_d1.1578481
X-RAY DIFFRACTIONf_dihedral_angle_d16.0422123
X-RAY DIFFRACTIONf_chiral_restr0.074986
X-RAY DIFFRACTIONf_plane_restr0.0051085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0043-2.03180.36621020.32282175X-RAY DIFFRACTION82
2.0318-2.06070.28971210.30392624X-RAY DIFFRACTION100
2.0607-2.09150.33881270.29952639X-RAY DIFFRACTION100
2.0915-2.12410.3281330.27572626X-RAY DIFFRACTION100
2.1241-2.15890.31781530.26132597X-RAY DIFFRACTION100
2.1589-2.1960.32471410.25682636X-RAY DIFFRACTION100
2.196-2.23590.30741530.25462603X-RAY DIFFRACTION100
2.2359-2.27880.30251380.2482600X-RAY DIFFRACTION100
2.2788-2.32520.26591500.24012649X-RAY DIFFRACTION100
2.3252-2.37570.30351130.24022629X-RAY DIFFRACTION100
2.3757-2.43080.30421540.24362620X-RAY DIFFRACTION100
2.4308-2.49140.30791370.2342634X-RAY DIFFRACTION100
2.4914-2.55860.30071600.23262587X-RAY DIFFRACTION100
2.5586-2.63370.26411360.23092626X-RAY DIFFRACTION100
2.6337-2.71840.271300.2372633X-RAY DIFFRACTION100
2.7184-2.81520.31091540.23962618X-RAY DIFFRACTION100
2.8152-2.92740.26511350.22912638X-RAY DIFFRACTION100
2.9274-3.06010.27431450.22992638X-RAY DIFFRACTION100
3.0601-3.22050.27171460.21962628X-RAY DIFFRACTION100
3.2205-3.4210.24171310.21722639X-RAY DIFFRACTION100
3.421-3.6830.26421440.20362633X-RAY DIFFRACTION100
3.683-4.04970.2191400.1912655X-RAY DIFFRACTION100
4.0497-4.62690.19421360.16632658X-RAY DIFFRACTION100
4.6269-5.79630.19271570.17872647X-RAY DIFFRACTION100
5.7963-17.89380.24681420.22382679X-RAY DIFFRACTION99
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)
10.82970.3079-0.03270.70490.13731.0683-0.05980.22680.0971-0.06230.0745-0.00540.0002-0.1-0.03140.1556-0.00940.00970.24980.00390.163438.738833.135943.5763
20.96970.2395-0.22470.2676-0.02030.7468-0.03910.1790.1025-0.01440.03050.0164-0.0212-0.2338-0.01310.1752-0.0054-0.01890.29720.02740.160218.802628.749958.5872
30.38050.23630.04450.49760.00760.0353-0.0106-0.0019-0.1326-0.02130.0092-0.04050.0996-0.0420.00150.10390.0053-0.00810.04630.010.105141.593129.327785.0272
40.9093-0.4533-0.10570.6855-0.09050.7153-0.025-0.26380.07230.0510.07710.0202-0.0273-0.0054-0.06150.05280.00090.01640.12850.01180.072320.645833.205899.7095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA11 - 770
2X-RAY DIFFRACTION2CHAIN BB1 - 768
3X-RAY DIFFRACTION3CHAIN CC1 - 759
4X-RAY DIFFRACTION4CHAIN DD12 - 765

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