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- PDB-4wei: Crystal structure of the F4 fimbrial adhesin FaeG in complex with... -

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Basic information

Entry
Database: PDB / ID: 4wei
TitleCrystal structure of the F4 fimbrial adhesin FaeG in complex with lactose
ComponentsK88 fimbrial protein AD
KeywordsSTRUCTURAL PROTEIN / Co-complex / Lectin / Adhesin / Immunoglobulin-like fold
Function / homologypilus / alpha-lactose / K88 fimbrial protein AD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 10, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 AD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5332
Polymers29,1901
Non-polymers3421
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint5 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.194, 93.194, 110.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 29190.352 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: pDEST / Details (production host): Gateway technology / Production host: Escherichia coli (E. coli) / References: UniProt: P14191
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Trizma/Bicine pH 8.5, 0.03 M of each halogen (sodium fluoride, sodium bromide, sodium iodide), 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350

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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 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→47.67 Å / Num. obs: 22359 / % possible obs: 99.9 % / Redundancy: 8.7 % / Net I/σ(I): 19.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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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: 2.3→47.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.043 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23029 1143 5.1 %RANDOM
Rwork0.19243 ---
obs0.19438 21174 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.888 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0 Å2
2---0.61 Å20 Å2
3---1.21 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 23 108 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021980
X-RAY DIFFRACTIONr_bond_other_d0.0010.021852
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.9642694
X-RAY DIFFRACTIONr_angle_other_deg0.84934255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90625.76978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22715305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.978155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
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_it2.4263.051049
X-RAY DIFFRACTIONr_mcbond_other2.4233.0491048
X-RAY DIFFRACTIONr_mcangle_it3.4194.5671313
X-RAY DIFFRACTIONr_mcangle_other3.4184.5681314
X-RAY DIFFRACTIONr_scbond_it3.6083.467931
X-RAY DIFFRACTIONr_scbond_other3.6063.467932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1845.0451382
X-RAY DIFFRACTIONr_long_range_B_refined6.6225.3642145
X-RAY DIFFRACTIONr_long_range_B_other6.61925.1072115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 86 -
Rwork0.342 1532 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: 36.0925 Å / Origin y: 9.1549 Å / Origin z: -13.285 Å
111213212223313233
T0.0456 Å2-0.0153 Å20.0369 Å2-0.0308 Å2-0.0016 Å2--0.0388 Å2
L2.7404 °2-1.0257 °20.9874 °2-1.4786 °2-0.3412 °2--1.7447 °2
S-0.0557 Å °-0.0027 Å °-0.0494 Å °0.0609 Å °-0.0523 Å °0.0875 Å °0.1223 Å °-0.0903 Å °0.108 Å °

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