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- PDB-5f8q: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 5f8q
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain S831 in complex with Nanobody Nb-ER19
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: 2.59 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.3Nov 6, 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
B: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19


Theoretical massNumber of molelcules
Total (without water)125,3584
Polymers125,3584
Non-polymers00
Water93752
1
A: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19


Theoretical massNumber of molelcules
Total (without water)62,6792
Polymers62,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-6 kcal/mol
Surface area23590 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19


Theoretical massNumber of molelcules
Total (without water)62,6792
Polymers62,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-6 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.034, 132.138, 123.485
Angle α, β, γ (deg.)90.00, 94.90, 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: _ / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA35 - 46233 - 460
21ASNASNBC35 - 46233 - 460
12VALVALCB3 - 1142 - 113
22VALVALDD3 - 1142 - 113

NCS ensembles :
ID
1
2

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Components

#1: Protein Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen / Blood group antigen binding adhesin (BabA)


Mass: 49418.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In this hybrid construct the diversity loop 1 (DL1) of the Spanish specialist strain S831 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: Q6DSZ5
#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): WK6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.59→48.5 Å / Num. obs: 49587 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.4
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.3 / % possible all: 89.1

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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: 2.59→48.5 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 23.114 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.379 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23026 2487 5 %RANDOM
Rwork0.19472 ---
obs0.19655 47074 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.77 Å2
2--1.06 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.59→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7972 0 0 52 8024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.028115
X-RAY DIFFRACTIONr_bond_other_d0.0040.027576
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.94711035
X-RAY DIFFRACTIONr_angle_other_deg1.017317434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4151059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14326.074349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.574151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6491526
X-RAY DIFFRACTIONr_chiral_restr0.0820.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219527
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021841
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_it3.1474.4614254
X-RAY DIFFRACTIONr_mcbond_other3.1474.4614253
X-RAY DIFFRACTIONr_mcangle_it4.7226.6945307
X-RAY DIFFRACTIONr_mcangle_other4.7226.6955308
X-RAY DIFFRACTIONr_scbond_it3.6914.7393861
X-RAY DIFFRACTIONr_scbond_other3.6914.743862
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6786.9645729
X-RAY DIFFRACTIONr_long_range_B_refined7.31635.3238903
X-RAY DIFFRACTIONr_long_range_B_other7.31535.3138899
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)
11A231610.1
12B231610.1
21C64340.09
22D64340.09
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 129 -
Rwork0.426 2892 -
obs--80.41 %
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)
11.08881.0419-0.72563.4376-1.63641.51070.0494-0.04320.09540.12590.01150.1071-0.09880.0015-0.06090.06080.0616-0.05060.0839-0.04230.1141-13.3532-20.981-43.1227
21.33940.60470.61874.8271-2.11883.6621-0.0771-0.0558-0.14020.3327-0.0274-0.3184-0.01860.24480.10450.19350.0146-0.070.1148-0.03560.1265-8.2528-42.7047-16.4438
31.24191.341.07373.31011.78711.93650.12820.1087-0.2132-0.08840.1027-0.2360.34610.1278-0.2310.23780.0545-0.06820.07320.05610.195421.5502-38.8664-101.125
42.6469-0.1962-0.40774.11312.19234.129-0.1080.05430.11620.0706-0.02080.25910.1326-0.26040.12890.0084-0.0128-0.00950.03770.04380.135811.9122-15.644-76.864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 462
2X-RAY DIFFRACTION2C3 - 115
3X-RAY DIFFRACTION3B35 - 462
4X-RAY DIFFRACTION4D3 - 116

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