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- PDB-6gmm: Crystal structure of Helicobacter pylori adhesin LabA -

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Basic information

Entry
Database: PDB / ID: 6gmm
TitleCrystal structure of Helicobacter pylori adhesin LabA
Componentsadhesin LabA
KeywordsSUGAR BINDING PROTEIN / bacterial adhesin / lectin / Helicobacter pylori / gastric mucosa
Function / homologySabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Outer membrane beta-barrel protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsParaskevopoulou, V. / Overman, R.C. / Stolnik, S. / Winkler, S. / Gellert, P. / Falcone, F.H. / Schimpl, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L01646X United Kingdom
CitationJournal: Current Research in Structural Biology / Year: 2021
Title: Structural and binding characterization of the LacdiNAc-specific adhesin (LabA; HopD) exodomain from Helicobacter pylori
Authors: Paraskevopoulou, V. / Schimpl, M. / Overman, R.C. / Stolnik, S. / Chen, Y. / Nguyen, L. / Winkler, G.S. / Gellert, P. / Klassen, J.S. / Falcone, F.H.
History
DepositionMay 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 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
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: adhesin LabA


Theoretical massNumber of molelcules
Total (without water)48,7891
Polymers48,7891
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.860, 59.860, 264.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein adhesin LabA


Mass: 48788.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BW246_00440, BZL55_00170 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W0VQ30
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.59 % / Description: bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 28 % PEG 2000 MME, 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.056→49.537 Å / Num. obs: 31169 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 20.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.242 / Net I/σ(I): 8.1
Reflection shellResolution: 2.056→2.093 Å / Redundancy: 11 % / Rmerge(I) obs: 1.516 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1558 / CC1/2: 0.599 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZH7

4zh7


Resolution: 2.06→49.537 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.889 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.197 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.252 569 1.84 %RANDOM
Rwork0.205 ---
obs0.206 30994 100 %-
Displacement parametersBiso mean: 36.27 Å2
Baniso -1Baniso -2Baniso -3
1-4.6427 Å20 Å20 Å2
2--4.6427 Å20 Å2
3----9.2855 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.06→49.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 0 173 3402
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013284HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094466HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1101SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes477HARMONIC5
X-RAY DIFFRACTIONt_it3284HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion19.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion456SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4015SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.272 -1.91 %
Rwork0.251 2716 -
all0.252 2769 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -5.2603 Å / Origin y: 7.8779 Å / Origin z: -24.0345 Å
111213212223313233
T0.1813 Å2-0.0079 Å2-0.0147 Å2-0.2423 Å2-0.0185 Å2---0.0864 Å2
L0.3586 °20.0241 °2-0.139 °2-0.2659 °2-0.218 °2--3.5042 °2
S-0.0123 Å °-0.0727 Å °-0.0078 Å °-0.0188 Å °0.0469 Å °-0.0227 Å °0.0265 Å °0.1554 Å °-0.0346 Å °
Refinement TLS groupSelection details: { A|* }

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