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- PDB-4we2: Donor strand complemented FaeG of F4ab fimbriae -

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Basic information

Entry
Database: PDB / ID: 4we2
TitleDonor strand complemented FaeG of F4ab fimbriae
ComponentsK88 fimbrial protein AB
KeywordsSTRUCTURAL PROTEIN / Adhesin / Lectin / Immunoglobulin-like fold
Function / homologypilus / K88 fimbrial protein AB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMoonens, K. / Van den Broeck, I. / De Kerpel, M. / Deboeck, F. / Raymaekers, H. / Remaut, H. / De Greve, H.
Funding support Belgium, 2items
OrganizationGrant numberCountry
FWOG030411N Belgium
FWO - HerculesUABR/09/005 Belgium
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Functional Insight into the Carbohydrate Receptor Binding of F4 Fimbriae-producing Enterotoxigenic Escherichia coli.
Authors: Moonens, K. / Van den Broeck, I. / De Kerpel, M. / Deboeck, F. / Raymaekers, H. / Remaut, H. / De Greve, H.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K88 fimbrial protein AB


Theoretical massNumber of molelcules
Total (without water)29,1341
Polymers29,1341
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.639, 49.026, 54.468
Angle α, β, γ (deg.)90.00, 109.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein K88 fimbrial protein AB / K88 antigen / K88 pilin


Mass: 29134.211 Da / Num. of mol.: 1 / Fragment: UNP residues 40-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: faeG / Plasmid: pDEST14 / Details (production host): Gateway technology / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: P02970
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18 mM Na/K-phosphate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→51.43 Å / Num. obs: 41977 / % possible obs: 97.9 % / Redundancy: 3.1 % / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.8 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLR

3hlr


Resolution: 1.5→51.43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.774 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21396 2113 5 %RANDOM
Rwork0.1751 ---
obs0.17704 39847 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2---0.75 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.5→51.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 0 289 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021983
X-RAY DIFFRACTIONr_bond_other_d0.0010.021865
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.9472700
X-RAY DIFFRACTIONr_angle_other_deg0.9734280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29925.18581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16315311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.486158
X-RAY DIFFRACTIONr_chiral_restr0.130.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2691.2351060
X-RAY DIFFRACTIONr_mcbond_other1.2691.2341059
X-RAY DIFFRACTIONr_mcangle_it1.7891.8541329
X-RAY DIFFRACTIONr_mcangle_other1.7881.8551330
X-RAY DIFFRACTIONr_scbond_it2.2011.495923
X-RAY DIFFRACTIONr_scbond_other2.21.496924
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1962.1511371
X-RAY DIFFRACTIONr_long_range_B_refined6.45412.3642306
X-RAY DIFFRACTIONr_long_range_B_other6.37311.0492145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 126 -
Rwork0.26 2369 -
obs--79.18 %
Refinement TLS params.Method: refined / Origin x: 0.8153 Å / Origin y: -11.3537 Å / Origin z: 16.5151 Å
111213212223313233
T0.0058 Å2-0.0053 Å20.0059 Å2-0.0237 Å2-0.0192 Å2--0.017 Å2
L1.6867 °2-0.3634 °20.6393 °2-1.3929 °2-0.933 °2--2.4291 °2
S0.0359 Å °0.075 Å °-0.0674 Å °-0.0771 Å °0.0201 Å °-0.0563 Å °0.0454 Å °0.0992 Å °-0.056 Å °

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