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- PDB-5f7m: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 5f7m
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group H Lewis b hexasaccharide
Components
  • Adhesin binding fucosylated histo-blood group antigen
  • Nanobody Nb-ER19
KeywordsCELL ADHESION / Adhesin / Lectin / Nanobody / Complex
Function / homologySabA, 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 / Adhesin binding fucosylated histo-blood group antigen
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsMoonens, K. / Gideonsson, P. / Subedi, S. / Romao, E. / Oscarson, S. / Muyldermans, S. / Boren, T. / Remaut, H.
Funding support Belgium, Sweden, 6items
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 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: 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 / 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 / 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 / _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 / struct_ncs_dom_lim
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 / _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
Revision 2.2Oct 23, 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
B: Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2606
Polymers125,2604
Non-polymers2,0002
Water2,702150
1
A: Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6303
Polymers62,6302
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint18 kcal/mol
Surface area23710 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6303
Polymers62,6302
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint19 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.096, 131.889, 123.102
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLYGLYAA35 - 46133 - 459
21ASNASNGLYGLYBB35 - 46133 - 459
12VALVALSERSERCC3 - 1142 - 113
22VALVALSERSERDD3 - 1142 - 113

NCS ensembles :
ID
1
2

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Components

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


Mass: 49369.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA2 / Variant: 17875 / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / References: UniProt: O52269
#2: Antibody Nanobody Nb-ER19


Mass: 13260.856 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): Top10
#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)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 999.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_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
[][b-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.: 150 / 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: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium nitrate, 0.1M Bis Tris propane pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.72→45 Å / Num. obs: 43591 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7
Reflection shellResolution: 2.72→2.89 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

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

5f7k


Resolution: 2.72→45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 22.627 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21767 2194 5 %RANDOM
Rwork0.17898 ---
obs0.18098 41291 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20.53 Å2
2--0.95 Å20 Å2
3----1.95 Å2
Refinement stepCycle: 1 / Resolution: 2.72→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 136 150 8260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028262
X-RAY DIFFRACTIONr_bond_other_d0.0040.027666
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.96611248
X-RAY DIFFRACTIONr_angle_other_deg0.992317622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68251060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01826.034348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.925151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4711526
X-RAY DIFFRACTIONr_chiral_restr0.0820.21326
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219536
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021846
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_it1.9042.6164258
X-RAY DIFFRACTIONr_mcbond_other1.9042.6164257
X-RAY DIFFRACTIONr_mcangle_it3.1813.9215312
X-RAY DIFFRACTIONr_mcangle_other3.1813.9225313
X-RAY DIFFRACTIONr_scbond_it2.6132.8754004
X-RAY DIFFRACTIONr_scbond_other2.6122.8754005
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2484.1925937
X-RAY DIFFRACTIONr_long_range_B_refined5.9420.6939227
X-RAY DIFFRACTIONr_long_range_B_other5.91220.6759206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A232950.09
12B232950.09
21C66060.05
22D66060.05
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 162 -
Rwork0.293 3008 -
obs--99 %
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)
11.29611.4416-0.93874.3847-2.01731.68410.0576-0.05520.10690.03580.02270.2004-0.0505-0.0234-0.08030.06650.0491-0.01940.1453-0.0560.03246.9471-19.621218.1547
21.313-1.44581.1433.9553-2.0381.97870.0694-0.1068-0.1570.13170.14010.28920.2556-0.1199-0.20950.1861-0.05720.01290.1487-0.07170.08049.361927.010839.7351
32.27850.17920.93986.0565-2.38194.1657-0.0947-0.0554-0.18240.34060.0459-0.2693-0.08130.16390.04880.18640.0117-0.04490.1132-0.0050.035712.0852-42.197845.0595
42.76840.4279-0.61425.4694-2.67584.0198-0.1364-0.07090.2482-0.1429-0.0044-0.36820.14990.12960.14080.0306-0.01690.01940.0337-0.03270.078118.962950.938615.2299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 462
2X-RAY DIFFRACTION2B35 - 463
3X-RAY DIFFRACTION3C3 - 115
4X-RAY DIFFRACTION4D3 - 116

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