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- PDB-8r4p: Structure of BabA from Helicobacter pylori strain 17875 -

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Basic information

Entry
Database: PDB / ID: 8r4p
TitleStructure of BabA from Helicobacter pylori strain 17875
ComponentsAdhesin binding fucosylated histo-blood group antigen
KeywordsCELL ADHESION / ADHESIN / LECTIN
Function / homologySabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / : / Adhesin binding fucosylated histo-blood group antigen
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPersson, K. / Boren, T. / Bugaytsova, J.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2022-01295 Sweden
CancerfondenCAN 21/1875 Sweden
CitationJournal: To Be Published
Title: Structure of BabA from Helicobacter pylori strain 17875
Authors: Persson, K. / Boren, T. / Bugaytsova, J.
History
DepositionNov 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,40611
Polymers61,2821
Non-polymers1,12410
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-48 kcal/mol
Surface area22140 Å2
Unit cell
Length a, b, c (Å)55.613, 96.953, 97.408
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 Adhesin binding fucosylated histo-blood group antigen


Mass: 61281.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 17875 / Gene: babA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O52269
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M cadmium chloride 0.1 M sodium acetate pH 4.6 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→36.64 Å / Num. obs: 35796 / % possible obs: 98.53 % / Redundancy: 4.5 % / Biso Wilson estimate: 33.89 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07556 / Rpim(I) all: 0.03854 / Rrim(I) all: 0.08534 / Net I/σ(I): 13.83
Reflection shellResolution: 2→2.071 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.9625 / Num. unique obs: 3574 / CC1/2: 0.535 / CC star: 0.835 / Rpim(I) all: 0.4935 / Rrim(I) all: 1.089 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.64 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1783 4.98 %
Rwork0.2106 --
obs0.2124 35794 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3599 0 10 205 3814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023660
X-RAY DIFFRACTIONf_angle_d0.4614982
X-RAY DIFFRACTIONf_dihedral_angle_d4.086506
X-RAY DIFFRACTIONf_chiral_restr0.035584
X-RAY DIFFRACTIONf_plane_restr0.002662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28581360.27122618X-RAY DIFFRACTION100
2.05-2.110.3441400.27442610X-RAY DIFFRACTION100
2.11-2.180.30861380.25232582X-RAY DIFFRACTION100
2.18-2.260.27391350.24532617X-RAY DIFFRACTION100
2.26-2.350.27461360.22792615X-RAY DIFFRACTION100
2.35-2.460.24711350.2162606X-RAY DIFFRACTION99
2.46-2.590.25271360.2262618X-RAY DIFFRACTION99
2.59-2.750.26181320.22022548X-RAY DIFFRACTION96
2.75-2.960.27361380.21392619X-RAY DIFFRACTION98
2.96-3.260.25121360.21572631X-RAY DIFFRACTION99
3.26-3.730.22831400.19832629X-RAY DIFFRACTION98
3.73-4.70.20551370.17292615X-RAY DIFFRACTION97
4.7-36.640.24331440.20892703X-RAY DIFFRACTION95

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