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- PDB-5f9a: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 5f9a
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain P436 in complex with blood group H Lewis b hexasaccharide
Components
  • Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
  • Nanobody Nb-ER19
KeywordsCELL ADHESION / Adhesin / Lectin / Nanobody / Complex
Function / homology
Function and homology information


SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adhesin binding fucosylated histo-blood group antigen / Adhesin
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsMoonens, K. / Gideonsson, P. / Subedi, S. / Romao, E. / Oscarson, S. / Muyldermans, S. / Boren, T. / Remaut, H.
Funding support Belgium, Sweden, 5items
OrganizationGrant numberCountry
Flanders Institute of Biotechnology (VIB)PRJ9 Belgium
Flanders Science Foundation (FWO)Odysseus program Belgium
Hercules FoundationUABR/09/005 Belgium
Vetenskapsradet/VR Sweden
Cancerfonden Sweden
CitationJournal: Cell Host Microbe / Year: 2016
Title: Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.
Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / ...Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / Coppens, F. / Lo, A.W. / Ny, T. / Solnick, J.V. / Vandenbussche, G. / Oscarson, S. / Hammarstrom, L. / Arnqvist, A. / Berg, D.E. / Muyldermans, S. / Boren, T. / Remaut, H.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1613
Polymers62,1622
Non-polymers1,0001
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint15 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.047, 136.167, 124.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen


Mass: 48900.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: In this hybrid construct the insertion domain of the Peruvian strain P436 (residues 179 to 258, responsible for carbohydrate binding) was grafted into the framework of the generalist strain 17875
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA2, babA / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / References: UniProt: O52269, UniProt: Q6DT10
#2: Antibody Nanobody Nb-ER19


Mass: 13260.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 999.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1a_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2-4-4/a4-b1_b3-c1_c3-d1_c4-f1_d2-e1WURCSPDB2Glycan 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]{}}[(4+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M Sodium acetate, 100 mM Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.44→51.54 Å / Num. obs: 39582 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.8
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F7K

5f7k


Resolution: 2.44→51.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.014 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25744 1996 5.1 %RANDOM
Rwork0.2048 ---
obs0.2073 37277 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.443 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20 Å2
2--0.9 Å20 Å2
3----1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.44→51.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 68 45 4079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.024121
X-RAY DIFFRACTIONr_bond_other_d0.0010.023806
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9655617
X-RAY DIFFRACTIONr_angle_other_deg0.98838744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29426.011178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2815642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7051513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
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_it2.8813.8332123
X-RAY DIFFRACTIONr_mcbond_other2.8793.8332122
X-RAY DIFFRACTIONr_mcangle_it4.3015.7422649
X-RAY DIFFRACTIONr_mcangle_other4.35.7432650
X-RAY DIFFRACTIONr_scbond_it3.9754.3191998
X-RAY DIFFRACTIONr_scbond_other3.9754.3191998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9976.3112968
X-RAY DIFFRACTIONr_long_range_B_refined7.3431.0814531
X-RAY DIFFRACTIONr_long_range_B_other7.33931.0854532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 147 -
Rwork0.412 2666 -
obs--97.61 %
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)
10.6675-0.77560.5673.544-1.88861.66280.04480.10680.0145-0.0636-0.0582-0.09750.12440.1260.01350.0170.0321-0.01490.1124-0.06320.04615.6272162.7361260.6019
22.0507-0.126-0.44074.5276-2.52253.4949-0.05590.02690.0143-0.2957-0.175-0.26340.20560.23550.23080.07310.04550.070.1578-0.00670.098123.5811183.663234.8284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 460
2X-RAY DIFFRACTION2C3 - 115

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