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- PDB-4zh7: Structural basis of Lewisb antigen binding by the Helicobacter py... -

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Basic information

Entry
Database: PDB / ID: 4zh7
TitleStructural basis of Lewisb antigen binding by the Helicobacter pylori adhesin BabA
ComponentsOuter membrane protein-adhesin
KeywordsSUGAR BINDING PROTEIN / blood group antigen binding / adhesin / Lewisb
Function / homologySabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Outer membrane protein-adhesin
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsHoward, T. / Hage, N. / Phillips, C. / Brassington, C.A. / Debreczeni, J. / Overman, R. / Gellert, P. / Stolnik, S. / Winkler, G.S. / Falcone, F.H.
CitationJournal: Sci Adv / Year: 2015
Title: Structural basis of Lewis(b) antigen binding by the Helicobacter pylori adhesin BabA.
Authors: Hage, N. / Howard, T. / Phillips, C. / Brassington, C. / Overman, R. / Debreczeni, J. / Gellert, P. / Stolnik, S. / Winkler, G.S. / Falcone, F.H.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: 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.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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein-adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0892
Polymers58,2511
Non-polymers8381
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint20 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.590, 91.770, 96.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer membrane protein-adhesin / blood group antibody binding adhesin


Mass: 58251.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA, jhp_0833 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZKV2
#2: 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


Type: oligosaccharide / Mass: 837.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-3-3/a3-b1_b3-c1_b4-e1_c2-d1WURCSPDB2Glycan 1.1.0
[][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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 22% PEG 3350, 0.1 M PCTP (pH = 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.12→44.78 Å / Num. obs: 29319 / % possible obs: 98.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 11.8
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.643

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHO

4zho


Resolution: 2.12→44.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.047 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22259 1513 4.9 %RANDOM
Rwork0.17102 ---
obs0.17357 29319 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.888 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å2-0 Å2
2--3.04 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.12→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 57 157 3869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023774
X-RAY DIFFRACTIONr_bond_other_d0.0010.023494
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9575138
X-RAY DIFFRACTIONr_angle_other_deg1.00438020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.626.821173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82615609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.246158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02857
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_it2.2462.581937
X-RAY DIFFRACTIONr_mcbond_other2.2332.5771936
X-RAY DIFFRACTIONr_mcangle_it3.3883.8432416
X-RAY DIFFRACTIONr_mcangle_other3.3873.8462417
X-RAY DIFFRACTIONr_scbond_it3.2793.0011837
X-RAY DIFFRACTIONr_scbond_other3.2783.0031838
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1444.362723
X-RAY DIFFRACTIONr_long_range_B_refined6.54921.0394260
X-RAY DIFFRACTIONr_long_range_B_other6.51520.9664223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 86 -
Rwork0.224 2139 -
obs--99.15 %

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