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- PDB-6jho: The complex crystal structure of Cagbeta with CagZ revealed a nov... -

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Basic information

Entry
Database: PDB / ID: 6jho
TitleThe complex crystal structure of Cagbeta with CagZ revealed a novel regulatory mechanism for T4SS coupling ATPase in Helicobacter pylori
Components
  • Cag pathogenicity island protein (Cag5)
  • Cag pathogenicity island protein (Cag6)
KeywordsCOUPLING PROTEIN / Complex crystal structure / CagZ / Cagbeta / Helicobacter pylori / type IV secretion system / STRUCTURAL PROTEIN
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
CAG pathogenicity island protein, CagZ / Type IV secretion system protein TraG/VirD4 / Cag pathogenicity island protein, CagZ / Cag-Z superfamily / Type IV secretory system Conjugative DNA transfer / CagZ / Delta-Endotoxin; domain 1 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Cag pathogenicity island protein (Cag5) / Cag pathogenicity island protein (Cag6)
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWu, X. / Zhao, Y. / Sun, L. / Ye, X. / Jiang, M. / Wang, Q. / Wang, Q. / Wu, Y.
CitationJournal: To Be Published
Title: The complex crystal structure of Cagbeta with CagZ revealed a novel regulatory mechanism in VirD4 coupling ATPase
Authors: Wu, X. / Zhao, Y. / Sun, L. / Ye, R. / Wu, Y.
History
DepositionFeb 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Cag pathogenicity island protein (Cag6)
B: Cag pathogenicity island protein (Cag6)
C: Cag pathogenicity island protein (Cag5)
D: Cag pathogenicity island protein (Cag5)


Theoretical massNumber of molelcules
Total (without water)94,7954
Polymers94,7954
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.298, 96.298, 212.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cag pathogenicity island protein (Cag6)


Mass: 23815.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_0526 / Variant: ATCC 700392 / 26695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25261
#2: Protein Cag pathogenicity island protein (Cag5)


Mass: 23581.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_0524 / Variant: ATCC 700392 / 26695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25260
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: CAPSO, PEG8k, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.97775 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 68411 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Χ2: 0.501 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0310.31.56233390.5430.4881.6390.44699
2.03-2.0711.31.23133530.6190.3671.2860.54999.6
2.07-2.1112.11.05233430.8140.3011.0950.46899.8
2.11-2.1512.30.83533540.8490.2370.8690.46399.9
2.15-2.212.30.61833880.9110.1760.6440.44999.7
2.2-2.2512.30.59333430.9080.170.6180.58799.8
2.25-2.3112.20.46433880.9520.1340.4830.46899.9
2.31-2.3712.10.36733720.9660.1060.3830.46599.9
2.37-2.4411.70.30133780.9720.090.3150.477100
2.44-2.5211.70.24633970.9820.0740.2570.49100
2.52-2.6112.50.19734090.9890.0570.2050.48899.9
2.61-2.7112.70.18133740.9910.0520.1880.52499.9
2.71-2.8412.70.14234310.9940.0410.1480.49399.9
2.84-2.9912.80.1133960.9960.0320.1140.505100
2.99-3.1712.20.08734340.9970.0260.0910.522100
3.17-3.4212.70.06534560.9980.0190.0680.537100
3.42-3.7613.50.05434450.9990.0150.0570.568100
3.76-4.3113.20.04234940.9990.0120.0440.54100
4.31-5.4312.60.03935490.9990.0110.040.506100
5.43-5012.20.03437680.9990.010.0360.448100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S2X

1s2x


Resolution: 2.1→48.149 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95
RfactorNum. reflection% reflection
Rfree0.2211 2986 5.04 %
Rwork0.1908 --
obs0.1923 59190 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.59 Å2 / Biso mean: 42.1509 Å2 / Biso min: 20.62 Å2
Refinement stepCycle: final / Resolution: 2.1→48.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6014 0 0 370 6384
Biso mean---44.98 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086124
X-RAY DIFFRACTIONf_angle_d0.8268249
X-RAY DIFFRACTIONf_chiral_restr0.049899
X-RAY DIFFRACTIONf_plane_restr0.0051080
X-RAY DIFFRACTIONf_dihedral_angle_d3.833707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.13440.2841420.234326362778
2.1344-2.17120.23481330.227126012734
2.1712-2.21070.2621550.221326282783
2.2107-2.25320.25721480.224325982746
2.2532-2.29920.2691470.214826422789
2.2992-2.34920.22261420.2126562798
2.3492-2.40390.25921470.20826152762
2.4039-2.4640.28011470.211826212768
2.464-2.53060.25561420.212926762818
2.5306-2.60510.24711340.208826362770
2.6051-2.68910.25881320.204926572789
2.6891-2.78520.23961300.209926652795
2.7852-2.89680.22481410.211826732814
2.8968-3.02860.22851300.210726752805
3.0286-3.18820.24271460.213126632809
3.1882-3.38790.22411420.198226942836
3.3879-3.64940.20461570.1926792836
3.6494-4.01650.21251230.178627482871
4.0165-4.59730.17611500.153827262876
4.5973-5.79060.21261390.174927752914
5.7906-48.16160.19441590.169229403099

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