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- PDB-4zh0: Structure of Helicobacter pylori adhesin BabA determined by SeMet SAD -

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Basic information

Entry
Database: PDB / ID: 4zh0
TitleStructure of Helicobacter pylori adhesin BabA determined by SeMet SAD
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 / SAD / Resolution: 1.91 Å
AuthorsHoward, T.D. / 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 1.3Nov 6, 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

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Assembly

Deposited unit
A: Outer membrane protein-adhesin


Theoretical massNumber of molelcules
Total (without water)58,4861
Polymers58,4861
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.830, 93.040, 96.920
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 antigen-binding adhesin


Mass: 58485.543 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 22% PEG 3350, 0.2M Ammonium Acetate, 0.1M Citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→67.12 Å / Num. obs: 39877 / % possible obs: 96.7 % / Redundancy: 23.1 % / Rmerge(I) obs: 0.236 / Net I/σ(I): 13.2
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 13.8 % / Rmerge(I) obs: 3.43 / Mean I/σ(I) obs: 0.9 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SHELXDEphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.91→67.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.366 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23039 2071 4.9 %RANDOM
Rwork0.18835 ---
obs0.19044 39877 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--1.25 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 1.91→67.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 0 133 3795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023721
X-RAY DIFFRACTIONr_bond_other_d0.0020.023460
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9425058
X-RAY DIFFRACTIONr_angle_other_deg1.01837955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5285483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08226.821173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25415597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.966158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024419
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_it2.7233.0951941
X-RAY DIFFRACTIONr_mcbond_other2.7113.0931940
X-RAY DIFFRACTIONr_mcangle_it3.6354.6212421
X-RAY DIFFRACTIONr_mcangle_other3.6354.6232422
X-RAY DIFFRACTIONr_scbond_it4.4153.621780
X-RAY DIFFRACTIONr_scbond_other4.4143.6211781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6185.2332638
X-RAY DIFFRACTIONr_long_range_B_refined7.90825.3484206
X-RAY DIFFRACTIONr_long_range_B_other7.90525.2874176
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 102 -
Rwork0.387 1864 -
obs--62.39 %

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