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- PDB-4dvz: Crystal structure of the Helicobacter pylori CagA oncoprotein -

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Basic information

Entry
Database: PDB / ID: 4dvz
TitleCrystal structure of the Helicobacter pylori CagA oncoprotein
ComponentsCytotoxicity-associated immunodominant antigen
KeywordsONCOPROTEIN
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 / MAD / Resolution: 3.19 Å
AuthorsHayashi, T. / Senda, M. / Morohashi, H. / Higashi, H. / Horio, M. / Kashiba, Y. / Nagase, L. / Sasaya, D. / Shimizu, T. / Venugopalan, N. ...Hayashi, T. / Senda, M. / Morohashi, H. / Higashi, H. / Horio, M. / Kashiba, Y. / Nagase, L. / Sasaya, D. / Shimizu, T. / Venugopalan, N. / Kumeta, H. / Noda, N. / Inagaki, F. / Senda, T. / Hatakeyama, M.
CitationJournal: Cell Host Microbe / Year: 2012
Title: Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA
Authors: Hayashi, T. / Senda, M. / Morohashi, H. / Higashi, H. / Horio, M. / Kashiba, Y. / Nagase, L. / Sasaya, D. / Shimizu, T. / Venugopalan, N. / Kumeta, H. / Noda, N.N. / Inagaki, F. / Senda, T. / Hatakeyama, M.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)63,6251
Polymers63,6251
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)95.671, 95.671, 167.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytotoxicity-associated immunodominant antigen / CagA / CAG pathogenicity island protein 26


Mass: 63625.383 Da / Num. of mol.: 1 / Fragment: UNP residues 261-829
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: cagA / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7% EtOH, 50mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98057, 0.98086
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2011
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980571
20.980861
ReflectionResolution: 3.19→74.3 Å / Num. all: 15242 / Num. obs: 15242 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 97.02 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 33.39
Reflection shellResolution: 3.19→3.37 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 6 / Num. unique all: 2263 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.19→74.3 Å / Cor.coef. Fo:Fc: 0.9219 / Cor.coef. Fo:Fc free: 0.8671 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 1.611 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.553 / SU Rfree Blow DPI: 0.426 / SU Rfree Cruickshank DPI: 0.435 / Stereochemistry target values: BUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 1016 6.67 %RANDOM
Rwork0.2215 ---
all0.2253 15242 --
obs0.2253 15242 99.28 %-
Displacement parametersBiso max: 186.4 Å2 / Biso mean: 103.74 Å2 / Biso min: 56 Å2
Baniso -1Baniso -2Baniso -3
1-11.2947 Å20 Å20 Å2
2--11.2947 Å20 Å2
3----22.5895 Å2
Refine analyzeLuzzati coordinate error obs: 0.799 Å
Refinement stepCycle: LAST / Resolution: 3.19→74.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 0 0 3635
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1385SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3671HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
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_contact4061SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3671HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4902HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion24.69
LS refinement shellResolution: 3.19→3.41 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3041 199 7.35 %
Rwork0.2478 2508 -
all0.2518 2707 -
obs--99.28 %

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