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- PDB-5f7k: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 5f7k
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with Nanobody Nb-ER19
Components
  • 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
PHOSPHATE ION / Adhesin binding fucosylated histo-blood group antigen
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Non-polymer description
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
C: Nanobody Nb-ER19
B: Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4407
Polymers125,2604
Non-polymers1803
Water8,665481
1
A: Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8105
Polymers62,6302
Non-polymers1803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-22 kcal/mol
Surface area23720 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19


Theoretical massNumber of molelcules
Total (without water)62,6302
Polymers62,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-6 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 131.660, 123.460
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
11ASNASNGLYGLYAA32 - 46130 - 459
21ASNASNGLYGLYBC32 - 46130 - 459
12VALVALSERSERCB3 - 1142 - 113
22VALVALSERSERDD3 - 1142 - 113

NCS ensembles :
ID
1
2

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#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): WK6

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Non-polymers , 4 types, 484 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2 / Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA2 / Variant: 17875 / Production host: Escherichia coli (E. coli) / Variant (production host): Top10
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.42 Å3/Da / Density % sol: 64 %
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: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.17→58.04 Å / Num. obs: 85215 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.6
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→58.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.463 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20654 4261 5 %RANDOM
Rwork0.17074 ---
obs0.17259 80920 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.14 Å2
2--0.2 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.17→58.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8000 0 10 481 8491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.028180
X-RAY DIFFRACTIONr_bond_other_d0.0060.027609
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.94611119
X-RAY DIFFRACTIONr_angle_other_deg1.186317515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36951068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00226.056355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.745151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0731526
X-RAY DIFFRACTIONr_chiral_restr0.1090.21271
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219612
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021866
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_it2.8423.3084278
X-RAY DIFFRACTIONr_mcbond_other2.8423.3084277
X-RAY DIFFRACTIONr_mcangle_it3.8944.9415338
X-RAY DIFFRACTIONr_mcangle_other3.8934.9415339
X-RAY DIFFRACTIONr_scbond_it4.0653.6933902
X-RAY DIFFRACTIONr_scbond_other3.9813.6873899
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7975.3585774
X-RAY DIFFRACTIONr_long_range_B_refined8.04227.4959556
X-RAY DIFFRACTIONr_long_range_B_other8.03427.1159395
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)
11A229880.11
12B229880.11
21C64100.08
22D64100.08
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 333 -
Rwork0.268 6012 -
obs--100 %
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)
11.00891.0037-0.66883.177-1.39271.3090.0449-0.02690.0783-0.00410.00120.1536-0.0554-0.0283-0.04610.08210.0551-0.00860.1428-0.03530.0181-13.3449-21.1694-42.7973
21.96920.3990.34733.9643-1.58912.52430.0185-0.0713-0.12180.2771-0.0479-0.1404-0.00290.12310.02940.18190.0111-0.04060.157500.034-8.441-42.6343-16.292
31.03461.20570.87383.03671.50481.71170.04330.072-0.1366-0.17840.1319-0.24030.22470.1094-0.17520.1270.04950.01360.13920.04640.079121.078-38.33-100.8411
41.75720.1756-0.27664.03032.12252.7511-0.05050.02960.07350.1826-0.04350.2201-0.0025-0.06860.0940.02240.01940.0210.10310.05130.054811.6912-15.5029-76.7656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 462
2X-RAY DIFFRACTION2C3 - 115
3X-RAY DIFFRACTION3B32 - 463
4X-RAY DIFFRACTION4D3 - 116

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