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- PDB-4g0h: Crystal structure of the N-terminal domain of Helicobacter pylori... -

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Basic information

Entry
Database: PDB / ID: 4g0h
TitleCrystal structure of the N-terminal domain of Helicobacter pylori CagA protein
ComponentsCytotoxicity-associated immunodominant antigen
KeywordsTOXIN / cytotoxin / integrin beta 1 / PROTEIN BINDING
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / toxin transmembrane transporter activity / molecular adaptor activity
Similarity search - Function
CagA exotoxin domain III / Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytotoxicity-associated immunodominant antigen
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsKaplan-Turkoz, B. / Remaut, H. / Dian, C. / Louche, A. / Terradot, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural insights into Helicobacter pylori oncoprotein CagA interaction with beta 1 integrin.
Authors: Kaplan-Turkoz, B. / Jimenez-Soto, L.F. / Dian, C. / Ertl, C. / Remaut, H. / Louche, A. / Tosi, T. / Haas, R. / Terradot, L.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)103,0051
Polymers103,0051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.830, 97.830, 245.390
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 Cytotoxicity-associated immunodominant antigen / 120 kDa protein / CAG pathogenicity island protein 26


Mass: 103005.117 Da / Num. of mol.: 1 / Fragment: UNP residues 1 to 884
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: cag26, cagA, cai, HP0547, HP_0547 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55980

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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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% Ethanol, Na Cacodylate 100mM pH7, NaI 15mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 2.3 / Number: 76085 / Rsym value: 0.07 / D res high: 3.8 Å / D res low: 91.256 Å / Num. obs: 12510 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
12.0298.3899.210.0430.0435
8.512.0299.910.0390.0396.1
6.948.599.610.0590.0595.5
6.016.9499.910.0920.0926.4
5.376.0199.910.1150.1155.9
4.915.3710010.1320.1326.1
4.544.9110010.1530.1536.5
4.254.5499.910.240.246.5
4.014.2599.710.4080.4085.7
3.84.0110010.8150.8156.3
ReflectionResolution: 3.6→90.874 Å / Num. all: 13408 / Num. obs: 13408 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rsym value: 0.076 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.6-3.793.60.8520.90.852196.4
3.79-4.023.60.4921.50.492195
4.02-4.33.50.2742.70.274192.6
4.3-4.653.20.1694.30.169186.7
4.65-5.093.60.1116.20.111195.6
5.09-5.693.60.1016.90.101194.9
5.69-6.573.30.10260.102189.9
6.57-8.053.30.0817.20.081190.3
8.05-11.383.30.04410.10.044193.6
11.38-81.7972.90.0479.50.047187.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1056refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.6→62.752 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.62 / σ(F): 1.37 / Phase error: 39.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3413 670 5.02 %
Rwork0.3287 --
obs0.3294 13345 91.79 %
all-13346 -
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.8307 Å2
Baniso -1Baniso -2Baniso -3
1--1.0268 Å20 Å20 Å2
2---1.0268 Å2-0 Å2
3---2.0537 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3.6→62.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 0 0 3275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023306
X-RAY DIFFRACTIONf_angle_d0.5934462
X-RAY DIFFRACTIONf_dihedral_angle_d11.3511149
X-RAY DIFFRACTIONf_chiral_restr0.042526
X-RAY DIFFRACTIONf_plane_restr0.002588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.87790.3571510.30392539X-RAY DIFFRACTION95
3.8779-4.26810.32551280.27252524X-RAY DIFFRACTION93
4.2681-4.88550.33141360.25112414X-RAY DIFFRACTION89
4.8855-6.15440.3471250.32632588X-RAY DIFFRACTION93
6.1544-62.76160.34251300.36552610X-RAY DIFFRACTION89

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