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- PDB-5f97: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 5f97
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain A730 in complex with blood group A type 1 hexasaccharide
Components
  • Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
  • Nanbody 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: 2.62 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 1.2Sep 28, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / 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 / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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

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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
C: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
D: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
E: Nanbody Nb-ER19
F: Nanbody Nb-ER19
G: Nanbody Nb-ER19
H: Nanbody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,10212
Polymers252,8758
Non-polymers4,2284
Water1,35175
1
A: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
E: Nanbody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2763
Polymers63,2192
Non-polymers1,0571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint21 kcal/mol
Surface area24340 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
F: Nanbody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2763
Polymers63,2192
Non-polymers1,0571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint21 kcal/mol
Surface area24630 Å2
MethodPISA
3
C: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
G: Nanbody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2763
Polymers63,2192
Non-polymers1,0571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint23 kcal/mol
Surface area24090 Å2
MethodPISA
4
D: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
H: Nanbody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2763
Polymers63,2192
Non-polymers1,0571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint21 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.900, 134.910, 123.800
Angle α, β, γ (deg.)90.00, 102.52, 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 of the Alaskan strain A730 (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: Q6DSX7
#2: Antibody
Nanbody 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) / Variant (production host): WK6
#3: Polysaccharide
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/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-GalpNAc]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 61.76 %
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: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.62→67.46 Å / Num. obs: 98949 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.6
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 5.8 / % possible all: 99.9

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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: 2.62→67.46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 24.642 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23688 4878 4.9 %RANDOM
Rwork0.18817 ---
obs0.19057 94042 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.988 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-1 Å2
2---0.84 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: 1 / Resolution: 2.62→67.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16268 0 288 75 16631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216915
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215598
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.96523039
X-RAY DIFFRACTIONr_angle_other_deg0.898335882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7852160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47926.193746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.205152697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7651548
X-RAY DIFFRACTIONr_chiral_restr0.1050.22682
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023816
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_it3.0314.2668640
X-RAY DIFFRACTIONr_mcbond_other3.034.2668639
X-RAY DIFFRACTIONr_mcangle_it4.8296.3910782
X-RAY DIFFRACTIONr_mcangle_other4.8296.3910783
X-RAY DIFFRACTIONr_scbond_it3.5544.728275
X-RAY DIFFRACTIONr_scbond_other3.5544.728275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6356.92912252
X-RAY DIFFRACTIONr_long_range_B_refined7.49434.24418906
X-RAY DIFFRACTIONr_long_range_B_other7.49334.24318905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 355 -
Rwork0.305 6951 -
obs--99.89 %
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)
10.4912-0.6071-0.16871.52190.62460.43520.0531-0.13780.067-0.16070.0154-0.0893-0.06130.031-0.06850.0379-0.04590.02540.3226-0.00250.137679.122-18.488164.652
20.7204-0.876-0.48052.31920.86590.5020.0764-0.07150.0649-0.16830.03340.005-0.05920.0007-0.10980.0192-0.01030.00470.31070.03370.108228.172-8.186163.538
30.188-0.5310.36691.9645-0.83250.91650.07210.0022-0.0556-0.00050.02960.33810.2817-0.0546-0.10170.1434-0.04220.03570.2946-0.03850.175636.29-35.334220.104
40.1982-0.30880.3351.8548-0.87131.02530.0874-0.0059-0.0690.05440.13570.2670.2163-0.1002-0.22310.1182-0.0634-0.03040.2769-0.04620.207188.113-25.955218.892
52.5443-0.4217-0.71932.23221.64783.41810.04970.1366-0.1863-0.4501-0.18740.1497-0.0473-0.08320.13770.22290.0131-0.02860.18270.01480.042278.232-41.08137.576
61.0419-0.6619-0.1482.28391.63362.95570.14780.0002-0.2416-0.4638-0.09820.29250.0109-0.1472-0.04960.2289-0.0178-0.1550.27210.01620.132526.021-31.724136.876
70.9890.1035-0.04362.2547-2.2823.07620.01630.05270.0731-0.1565-0.0899-0.09070.25040.2690.07360.03620.0020.0220.3727-0.08380.097648.723-14.097194.774
81.98160.2283-0.27882.6037-1.4152.44420.05740.09990.052-0.00590.0272-0.1260.05040.024-0.08460.0089-0.040.01530.3579-0.14450.188101.576-4.245194.503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 466
2X-RAY DIFFRACTION2I32 - 466
3X-RAY DIFFRACTION3K32 - 466
4X-RAY DIFFRACTION4M32 - 466
5X-RAY DIFFRACTION5C3 - 116
6X-RAY DIFFRACTION6J3 - 117
7X-RAY DIFFRACTION7L3 - 116
8X-RAY DIFFRACTION8N3 - 115

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