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- PDB-4b4r: Crystal Structure of the lectin domain of F18 fimbrial adhesin Fe... -

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Basic information

Entry
Database: PDB / ID: 4b4r
TitleCrystal Structure of the lectin domain of F18 fimbrial adhesin FedF in complex with blood group B type 1 hexasaccharide
ComponentsF18 FIMBRIAL ADHESIN AC
KeywordsCELL ADHESION / FIMBRIAE / BACTERIAL ADHESINS / PROTEIN-CARBOHYDRATE INTERACTIONS / ABH BLOOD GROUP BINDING
Function / homologyJelly Rolls - #1210 / Jelly Rolls / Sandwich / Mainly Beta / F18 fimbrial adhesin AC
Function and homology information
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)34,6544
Polymers32,6222
Non-polymers2,0322
Water1,54986
1
A: F18 FIMBRIAL ADHESIN AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3272
Polymers16,3111
Non-polymers1,0161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F18 FIMBRIAL ADHESIN AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3272
Polymers16,3111
Non-polymers1,0161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.900, 54.700, 145.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein F18 FIMBRIAL ADHESIN AC / FEDF / FIMBRIAL ADHESIN FEDF


Mass: 16311.161 Da / Num. of mol.: 2 / Fragment: LECTIN DOMAIN, RESIDUES 35-185
Source method: isolated from a genetically manipulated source
Details: FEDF LECTIN DOMAIN COMPRISING RESIDUS 15-165 / Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Strain: 107/86 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q47212
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido- ...alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1015.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1a_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3-2-4-5/a4-b1_b3-c1_c3-d1_d2-e1_d3-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBLOOD GROUP B TYPE 1 HEXASACCHARIDE DERIVED FROM SUS SCROFA DOMESTICA. BLOOD GROUP DETERMINANT ...BLOOD GROUP B TYPE 1 HEXASACCHARIDE DERIVED FROM SUS SCROFA DOMESTICA. BLOOD GROUP DETERMINANT ACQUIRED FROM ELICITYL (FRANCE)

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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 growDetails: 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 25267 / % possible obs: 99 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B4P

4b4p


Resolution: 1.8→51.21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.841 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAINS WITH POOR OR MISSING ELECTRON DENSITY WERE MODELLED IN MOST LIKELY CONFORMER, WITH OCCUPANCY SET TO 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25557 1330 5 %RANDOM
Rwork0.2119 ---
obs0.21411 25267 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.752 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.46 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→51.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 138 86 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212388
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9943279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98324.78392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.204157
X-RAY DIFFRACTIONr_chiral_restr0.150.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211707
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1331.51415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81822289
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.883973
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1794.5984
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
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 98 -
Rwork0.259 1861 -
obs--100 %
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)
15.20011.10160.62763.49150.02893.2623-0.0818-0.41360.41710.1230.04910.074-0.185-0.19360.03270.16060.07050.03520.11660.00570.1593-10.38-4.33417.095
22.46560.31880.53960.63680.13521.22680.0654-0.13540.07740.1347-0.0011-0.0505-0.05490.1312-0.06440.13670.01550.01430.14050.02450.0769-0.346-11.81917.579
32.05050.27750.7911.61180.35532.48090.09770.1899-0.1434-0.04260.04950.02340.01720.0191-0.14720.11650.03280.01090.12260.050.0832-4.984-17.18410.084
48.16351.7718.13823.3882-3.864214.80940.4306-0.28190.06990.4664-0.33950.1123-0.24660.1723-0.09110.3489-0.00560.08780.32-0.01220.200310.49-7.97629.222
55.02370.8383.57532.33522.46139.2312-0.33450.37920.78860.07010.00980.2837-0.39290.34490.32460.1147-0.0027-0.00830.1240.08530.1776-3.018-5.35310.129
65.10050.4897-2.17631.7137-0.90873.628-0.3789-0.4408-0.4674-0.25780.0703-0.20270.76050.5760.30860.35680.05560.06490.12940.02220.1721-2.779-39.11516.198
78.82591.8702-7.73731.3318-2.580314.0909-0.6650.0322-0.3278-0.16450.39010.24690.9768-1.80840.27490.3144-0.08680.06830.50420.03110.2016-21.817-38.31823.775
82.84060.6262-1.51753.0958-1.32162.1913-0.10850.25390.0764-0.16230.21780.24940.204-0.224-0.10930.1871-0.002-0.01490.1040.02940.0678-9.188-29.63714.212
91.7539-0.1332-3.1792.2381-6.05749.3721-0.15690.2529-0.2627-0.0568-0.176-0.00790.29630.13680.3330.25-0.00130.03070.202-0.00130.16330.191-24.5740.11
107.11353.0413-5.66071.6231-2.11045.7647-0.21160.1489-0.055-0.1970.1423-0.01820.269-0.11010.06920.26430.0160.03240.10450.03750.083-5.37-34.60515.495
1125.4478.94732.77913.32243.385618.1834-0.202-2.6963-0.8987-0.2767-0.34140.30810.0189-1.29080.54340.17860.05260.05370.8560.2980.2368-19.222-37.07932.741
122.6007-0.9604-1.85281.53241.74666.5105-0.33590.1933-0.272-0.77510.27030.12980.6703-0.16270.06560.6772-0.1406-0.00810.1797-0.02580.1554-11.194-39.8498.139
137.06421.9488-9.41654.8209-5.461132.2259-0.7040.1301-0.7024-0.64590.2074-0.17121.3102-0.88740.49670.3143-0.05970.05640.0868-0.01350.2187-10.19-45.37316.202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 23
2X-RAY DIFFRACTION2A24 - 82
3X-RAY DIFFRACTION3A83 - 112
4X-RAY DIFFRACTION4A113 - 126
5X-RAY DIFFRACTION5A127 - 148
6X-RAY DIFFRACTION6B5 - 44
7X-RAY DIFFRACTION7B45 - 67
8X-RAY DIFFRACTION8B68 - 93
9X-RAY DIFFRACTION9B94 - 103
10X-RAY DIFFRACTION10B104 - 112
11X-RAY DIFFRACTION11B113 - 126
12X-RAY DIFFRACTION12B127 - 138
13X-RAY DIFFRACTION13B139 - 149

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