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- PDB-4b4p: Crystal Structure of the lectin domain of F18 fimbrial adhesin FedF. -

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Basic information

Entry
Database: PDB / ID: 4b4p
TitleCrystal Structure of the lectin domain of F18 fimbrial adhesin FedF.
ComponentsF18 FIMBRIAL ADHESIN AC
KeywordsCELL ADHESION / FIMBRIAE / BACTERIAL ADHESINS / PROTEIN-CARBOHYDRATE INTERACTIONS / ABH BLOOD GROUP BINDING / STEC / ETEC / SPR / MST / BSI
Function / homologyJelly Rolls - #1210 / Jelly Rolls / Sandwich / Mainly Beta / BROMIDE ION / F18 fimbrial adhesin AC
Function and homology information
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMoonens, K. / Bouckaert, J. / Coddens, A. / Tran, T. / Panjikar, S. / De Kerpel, M. / Cox, E. / Remaut, H. / De Greve, H.
Citation
Journal: Mol.Microbiol. / Year: 2012
Title: Structural Insight in Histo-Blood Group Binding by the F18 Fimbrial Adhesin Fedf.
Authors: Moonens, K. / Bouckaert, J. / Coddens, A. / Tran, T. / Panjikar, S. / De Kerpel, M. / Cox, E. / Remaut, H. / De Greve, H.
#1: Journal: Microb.Pathog. / Year: 1996
Title: Characterization of F18 Fimbrial Genes Fede and Fedf Involved in Adhesion and Length of Enterotoxemic Escherichia Coli Strain 107/86.
Authors: Imberechts, H. / Wild, P. / Charlier, G. / De Greve, H. / Lintermans, P. / Pohl, P.
History
DepositionJul 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references / Source and taxonomy
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
A: F18 FIMBRIAL ADHESIN AC
B: F18 FIMBRIAL ADHESIN AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,85317
Polymers32,6222
Non-polymers1,23115
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-43.8 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.181, 74.382, 98.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA7 - 557 - 55
21ALAALALEULEUBB7 - 557 - 55
12TYRTYRPROPROAA65 - 11465 - 114
22TYRTYRPROPROBB65 - 11465 - 114
13LYSLYSPROPROAA128 - 147128 - 147
23LYSLYSPROPROBB128 - 147128 - 147

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Components

#1: Protein F18 FIMBRIAL ADHESIN AC / FEDF


Mass: 16311.161 Da / Num. of mol.: 2 / Fragment: LECTIN DOMAIN, RESIDUES 35-185
Source method: isolated from a genetically manipulated source
Details: FRAGMENT ENCOMPASSES RESIDUES 15-165 OF MATURE FEDF PROTEIN
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Strain: 107/86 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q47212
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.17 M AMMONIUM SULFATE, 25.5% (W/V) PEG 4000 AND 15% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.77
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 1.8→19.81 Å / Num. obs: 24427 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rrim(I) all: 0.07 / Net I/σ(I): 28.83
Reflection shellHighest resolution: 1.8 Å / Mean I/σ(I) obs: 12.94 / Rrim(I) all: 0.185 / % possible all: 100

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Processing

Software
NameVersionClassification
SIGMAAmodel building
MLPHAREmodel building
XSCALEdata scaling
SHELXCDphasing
PHASERphasing
SIGMAAphasing
RESOLVEphasing
BP3phasing
ABSphasing
MLPHAREphasing
REFMAC5.2.0019refinement
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→19.81 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.601 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22078 1051 4.1 %RANDOM
Rwork0.17774 ---
obs0.17947 24427 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 23 176 2367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222232
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9263039
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.80924.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94615351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.389157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021685
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2941
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21502
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.251.51437
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1952.52258
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8425932
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.12410780
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
475tight positional0.130.05
431medium positional0.620.5
475tight thermal1.321.5
431medium thermal2.422.5
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 77 -
Rwork0.228 1753 -
obs--99.95 %

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