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- PDB-5f93: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 5f93
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain A730 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: 2.99 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 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
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 2.2Nov 20, 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
B: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
E: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
G: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
D: Nanobody Nb-ER19
F: Nanobody Nb-ER19
H: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,87412
Polymers252,8758
Non-polymers4,0004
Water75742
1
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)64,2193
Polymers63,2192
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint19 kcal/mol
Surface area24330 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2193
Polymers63,2192
Non-polymers1,0001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint19 kcal/mol
Surface area24570 Å2
MethodPISA
3
E: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
F: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2193
Polymers63,2192
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint21 kcal/mol
Surface area24190 Å2
MethodPISA
4
G: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
H: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2193
Polymers63,2192
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint19 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.175, 134.473, 123.979
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 49957.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: In this hybrid construct the insertion domain (residues 179-258) of the Alaskan strain A730, 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: Q6DSX7
#2: Antibody
Nanobody Nb-ER19


Mass: 13260.856 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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.: 4
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.: 42 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2- Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M Buffer System 2 (Sodium HEPES; MOPS (acid)) pH ...Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2- Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M Buffer System 2 (Sodium HEPES; MOPS (acid)) pH 7.5, 50 % v/v EDO_P8K (40% v/v Ethylene glycol; 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.99→48.64 Å / Num. obs: 65294 / % possible obs: 97.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.9
Reflection shellResolution: 2.99→3.16 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.7 / % possible all: 86.1

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Processing

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

5f7k


Resolution: 2.99→48.64 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 38.088 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23381 3241 5 %RANDOM
Rwork0.18107 ---
obs0.18371 62025 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.088 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20.01 Å2
2---0.71 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.99→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16179 0 272 42 16493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216788
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215483
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.96522861
X-RAY DIFFRACTIONr_angle_other_deg0.819335587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37552139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37526.138738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.537152672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5051548
X-RAY DIFFRACTIONr_chiral_restr0.0790.22666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023788
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_it3.425.0848583
X-RAY DIFFRACTIONr_mcbond_other3.4185.0848582
X-RAY DIFFRACTIONr_mcangle_it5.5547.61210704
X-RAY DIFFRACTIONr_mcangle_other5.5547.61210705
X-RAY DIFFRACTIONr_scbond_it3.9815.598205
X-RAY DIFFRACTIONr_scbond_other3.9815.598206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.528.2112155
X-RAY DIFFRACTIONr_long_range_B_refined8.69640.38918612
X-RAY DIFFRACTIONr_long_range_B_other8.69640.39118613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.994→3.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 166 -
Rwork0.362 3371 -
obs--72.2 %
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)
10.4649-0.382-0.28871.15280.51390.30540.0491-0.07350.0647-0.10750.0264-0.0156-0.02630.02-0.07560.0620.0013-0.02170.36380.01670.071380.4099-14.6344163.9437
20.3735-0.4452-0.22590.96840.42430.24020.0954-0.20120.0161-0.1311-0.0329-0.0249-0.05560.0713-0.06250.0485-0.0674-0.00690.4014-0.02330.0709131.5747-24.8859164.8912
30.09010.19320.20840.92380.5170.53790.036-0.0182-0.0347-0.06910.1083-0.15120.11490.0216-0.14440.12690.0494-0.03690.31340.02270.12489.111334.5943144.2087
40.07630.30480.1391.39460.74320.6474-0.0089-0.0355-0.03370.06140.0096-0.16940.18020.0303-0.00080.11660.04060.00970.34640.0360.1055141.159125.2084143.211
50.7086-0.4465-0.40781.82160.9961.85910.0266-0.1139-0.1304-0.47410.0330.2215-0.0246-0.0072-0.05960.2412-0.0092-0.12360.32810.01020.09778.3721-38.0614137.3858
61.1918-0.6643-0.65211.72551.58972.0980.0734-0.0711-0.0603-0.418-0.11730.0906-0.08790.00760.04390.25710.0393-0.04340.27490.01230.0102130.6266-47.5089137.7382
70.63530.2618-0.40520.7420.50041.29080.037-0.13810.0045-0.01550.06990.04360.00890.0682-0.10690.04570.0573-0.02270.44760.10560.176.042256.5173168.7193
80.29730.16120.25881.28261.16241.6932-0.0019-0.0770.07190.0398-0.00750.02790.1486-0.10550.00940.02970.0052-0.00740.44390.07380.0504129.152546.5957168.3661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 467
2X-RAY DIFFRACTION2B32 - 466
3X-RAY DIFFRACTION3E32 - 466
4X-RAY DIFFRACTION4G32 - 466
5X-RAY DIFFRACTION5C3 - 116
6X-RAY DIFFRACTION6D3 - 116
7X-RAY DIFFRACTION7F3 - 116
8X-RAY DIFFRACTION8H3 - 116

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