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- PDB-5f7l: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

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Basic information

Entry
Database: PDB / ID: 5f7l
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with Nanobody Nb-ER14
Components
  • Adhesin binding fucosylated histo-blood group antigen
  • Nanobody Nb-ER14
KeywordsCELL ADHESION / Adhesin / Lectin / Nanobody / Complex
Function / homologySabA, 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 / Adhesin binding fucosylated histo-blood group antigen
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Nanobody Nb-ER14
C: Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,88812
Polymers127,1204
Non-polymers7698
Water1,58588
1
A: Adhesin binding fucosylated histo-blood group antigen
B: Nanobody Nb-ER14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8485
Polymers63,5602
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-51 kcal/mol
Surface area21720 Å2
MethodPISA
2
C: Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0407
Polymers63,5602
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-54 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.402, 133.715, 201.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A57 - 458
2010C57 - 458
1020B1 - 120
2020D1 - 120

NCS ensembles :
ID
1
2

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Components

#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-ER14


Mass: 14190.646 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate, 0.1 M Sodium acetate 4.5, 50 % w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.74→47.4 Å / Num. obs: 31163 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.9
Reflection shellResolution: 2.74→2.88 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.7 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.74→47.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.385 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26486 1647 5.3 %RANDOM
Rwork0.21221 ---
obs0.21494 29458 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0 Å2
2--0.98 Å2-0 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 2.74→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7445 0 40 88 7573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027600
X-RAY DIFFRACTIONr_bond_other_d0.0030.026989
X-RAY DIFFRACTIONr_angle_refined_deg1.61.94510328
X-RAY DIFFRACTIONr_angle_other_deg0.973316088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81226.284331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.522151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7841520
X-RAY DIFFRACTIONr_chiral_restr0.0850.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028886
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021710
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_it1.5412.5913972
X-RAY DIFFRACTIONr_mcbond_other1.5392.5913971
X-RAY DIFFRACTIONr_mcangle_it2.5463.8844951
X-RAY DIFFRACTIONr_mcangle_other2.5463.8854952
X-RAY DIFFRACTIONr_scbond_it2.1452.8633628
X-RAY DIFFRACTIONr_scbond_other2.0382.823597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3474.1355330
X-RAY DIFFRACTIONr_long_range_B_refined4.90320.6188455
X-RAY DIFFRACTIONr_long_range_B_other4.90220.6138452
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 / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A21496
12C21496
21B6471
22D6471
LS refinement shellResolution: 2.736→2.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 124 -
Rwork0.297 1977 -
obs--91.51 %
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)
10.91940.0746-0.00011.3071-0.1923.0409-0.01420.14950.0149-0.14670.03780.01510.0804-0.0805-0.02360.1185-0.0176-0.01360.03570.00270.0022-2.695118.4793-52.4346
20.9656-0.75780.26661.71830.36137.5309-0.0429-0.31010.00190.15570.1085-0.0730.0304-0.1573-0.06570.13960.0142-0.04880.14620.00570.11130.664110.9347-11.9801
30.9582-0.0975-0.09171.3311-0.24753.03720.0083-0.1066-0.02210.18940.02830.0298-0.0447-0.0598-0.03650.10090.00860.00530.03010.0030.0015-23.76843.9392-48.0786
40.94941.14460.21631.58710.68087.9557-0.06130.275-0.0438-0.14920.1878-0.11220.0715-0.0177-0.12650.14720.00210.02410.20220.04260.102-19.919150.7295-89.2102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 458
2X-RAY DIFFRACTION2B1 - 121
3X-RAY DIFFRACTION3C57 - 459
4X-RAY DIFFRACTION4D1 - 124

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