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- PDB-8cb2: A complex of cagX and cagY components of Helicobacter pylori type... -

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Basic information

Entry
Database: PDB / ID: 8cb2
TitleA complex of cagX and cagY components of Helicobacter pylori type IV secretion system
Components
  • Cag pathogenicity island protein
  • Type IV secretion system apparatus protein CagY (Fragment)
KeywordsPROTEIN TRANSPORT / Helicobacter pylori / CagX_CTD / CagY_CTD / complex structure / interaction
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
DC-EC / DC-EC Repeat / Type IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI
Similarity search - Domain/homology
Type IV secretion system apparatus protein CagY / Cag pathogenicity island protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsIsupov, M.N. / Jiang, M. / Zhang, H. / Wu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A complex of cagX and cagY components of Helicobacter pylori type IV secretion system
Authors: Isupov, M.N. / Jiang, M.
History
DepositionJan 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Cag pathogenicity island protein
BBB: Type IV secretion system apparatus protein CagY (Fragment)
CCC: Cag pathogenicity island protein
DDD: Type IV secretion system apparatus protein CagY (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3945
Polymers95,3544
Non-polymers401
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-93 kcal/mol
Surface area39270 Å2
Unit cell
Length a, b, c (Å)55.059, 196.123, 200.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21CCC
32BBB
42DDD

NCS domain segments:

End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEAAAA17 - 15817 - 158
221ILEILECCCC17 - 15817 - 158
332GLUGLUBBBB7 - 2497 - 249
442GLUGLUDDDD7 - 2497 - 249

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Protein Cag pathogenicity island protein


Mass: 19163.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0528 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q75X32
#2: Protein Type IV secretion system apparatus protein CagY (Fragment)


Mass: 28513.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: cagY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A438QIF3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.2M Calcium acetate, 0.1M Bis-tris pH 5.5 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9689 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9689 Å / Relative weight: 1
ReflectionResolution: 2.7→49.08 Å / Num. obs: 30397 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.99 / Net I/σ(I): 5.9
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 3985 / CC1/2: 0.241 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
MOLREPphasing
DMphasing
Cootmodel building
BUSTERrefinement
ISOLDErefinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.079 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / SU B: 23.43 / SU ML: 0.436 / Cross valid method: FREE R-VALUE / ESU R: 0.781 / ESU R Free: 0.374 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.298 1515 4.99 %
Rwork0.2516 28848 -
all0.254 --
obs-30363 99.872 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 109.063 Å2
Baniso -1Baniso -2Baniso -3
1--2.086 Å2-0 Å20 Å2
2---3.732 Å2-0 Å2
3---5.818 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 0 1 1 6032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126143
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.6398298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94124.286273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.643151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6681521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024503
X-RAY DIFFRACTIONr_nbd_refined0.1990.22272
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0840.2164
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2990.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2350.21
X-RAY DIFFRACTIONr_mcbond_it8.48410.6833087
X-RAY DIFFRACTIONr_mcangle_it12.84115.993847
X-RAY DIFFRACTIONr_scbond_it9.31510.9823056
X-RAY DIFFRACTIONr_scangle_it14.03816.2554451
X-RAY DIFFRACTIONr_lrange_it19.224141.9528506
X-RAY DIFFRACTIONr_ncsr_local_group_10.1420.053944
X-RAY DIFFRACTIONr_ncsr_local_group_20.1080.056624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.141820.05007
12CCCX-RAY DIFFRACTIONLocal ncs0.141820.05007
23BBBX-RAY DIFFRACTIONLocal ncs0.108320.05007
24DDDX-RAY DIFFRACTIONLocal ncs0.108320.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.4521020.4392116X-RAY DIFFRACTION99.6406
2.77-2.8460.4181080.4212043X-RAY DIFFRACTION99.9071
2.846-2.9280.4211240.3991978X-RAY DIFFRACTION100
2.928-3.0180.361910.3651922X-RAY DIFFRACTION100
3.018-3.1170.3771100.3391881X-RAY DIFFRACTION100
3.117-3.2260.326750.3011844X-RAY DIFFRACTION100
3.226-3.3480.333750.2841767X-RAY DIFFRACTION100
3.348-3.4850.3291010.2581692X-RAY DIFFRACTION100
3.485-3.6390.278860.2541647X-RAY DIFFRACTION100
3.639-3.8170.358840.2381531X-RAY DIFFRACTION100
3.817-4.0230.321710.2311516X-RAY DIFFRACTION100
4.023-4.2670.256590.2021435X-RAY DIFFRACTION100
4.267-4.5610.261690.1991323X-RAY DIFFRACTION99.7849
4.561-4.9250.221720.1931235X-RAY DIFFRACTION100
4.925-5.3940.251660.2011146X-RAY DIFFRACTION100
5.394-6.0280.295700.2291042X-RAY DIFFRACTION100
6.028-6.9570.316520.241921X-RAY DIFFRACTION99.6926
6.957-8.510.255470.23797X-RAY DIFFRACTION100
8.51-11.9920.283360.22631X-RAY DIFFRACTION99.701
11.992-49.0790.293170.318381X-RAY DIFFRACTION96.368

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