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- PDB-8ynx: Crystal structure of Cag3-CagT complex from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 8ynx
TitleCrystal structure of Cag3-CagT complex from Helicobacter pylori
Components
  • Cag pathogenicity island protein 3
  • Cag pathogenicity island protein T
KeywordsSTRUCTURAL PROTEIN / Type IV secretion system / Helicobacter pylori
Function / homologyCag pathogenicity island protein Cag12 / Cag pathogenicity island protein Cag12 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Cag pathogenicity island protein 3 / Cag pathogenicity island protein T
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsMok, C.Y. / Au, S.W.N.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14121619 Hong Kong
CitationJournal: Structure / Year: 2024
Title: Structural insights into the assembly pathway of the Helicobacter pylori CagT4SS outer membrane core complex.
Authors: Mok, C.Y. / Chu, H.Y. / Lam, W.W.L. / Au, S.W.N.
History
DepositionMar 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cag pathogenicity island protein 3
B: Cag pathogenicity island protein T


Theoretical massNumber of molelcules
Total (without water)38,4472
Polymers38,4472
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-41 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.621, 112.621, 128.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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Components

#1: Protein Cag pathogenicity island protein 3


Mass: 24692.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: cag3, HPG27_481 / Production host: Escherichia coli (E. coli) / References: UniProt: B5Z6P5
#2: Protein Cag pathogenicity island protein T


Mass: 13754.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: cagT, HPG27_491 / Production host: Escherichia coli (E. coli) / References: UniProt: B5Z6Q4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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: 5.29 Å3/Da / Density % sol: 76.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus I A10 0.06M divalents mix, 0.1M buffer system 3, 30% v/v precipitant mix 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 3.25→29.13 Å / Num. obs: 13523 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 67.82 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.6
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1313 / CC1/2: 0.748 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→29.13 Å / SU ML: 0.3223 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.5993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2043 664 5 %
Rwork0.1744 12604 -
obs0.1759 13268 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.64 Å2
Refinement stepCycle: LAST / Resolution: 3.25→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 0 22 2060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122080
X-RAY DIFFRACTIONf_angle_d1.15552812
X-RAY DIFFRACTIONf_chiral_restr0.0609308
X-RAY DIFFRACTIONf_plane_restr0.0083362
X-RAY DIFFRACTIONf_dihedral_angle_d6.429271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.50.24431250.23612371X-RAY DIFFRACTION94.47
3.5-3.850.25641310.19812489X-RAY DIFFRACTION98.98
3.85-4.40.18941330.17142527X-RAY DIFFRACTION99.18
4.41-5.540.18711350.14542560X-RAY DIFFRACTION99.45
5.54-29.130.18921400.16592657X-RAY DIFFRACTION97.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.00048622542-3.12978519717-3.046961188935.112511609410.7528549823439.28785266459-0.05670095166490.345271433366-0.458833533106-0.171542097847-0.520806693327-0.7443760080.738899137960.6225327700540.4915132218730.5624695032910.1974035720270.1446450314920.5926775752950.1866386612150.68532583372934.6384608119-11.396481839119.6248734178
22.73307982923-3.571994696950.9749810297377.7035550852-4.51932008015.247196155030.1062428073230.602877973495-0.528100928149-1.52311833572-0.9182847006240.1056955263121.447698308711.485680867870.6347804553240.9942227948220.006122362128520.09795994935680.7531671922610.05191855360190.56050733387528.1649048687-1.58555196297.25205421169
32.52069560437-1.24240193676-1.279036740068.20846737957-6.878097539987.92696893953-0.0413941989123-0.006777473283380.2900402740820.2338139959840.2488206111730.538117648612-0.0588782985193-0.07411874996-0.1581975217140.35369185764-0.0106285047575-0.0007986775738220.389552113799-0.0333437089760.37253350896421.23858637386.7805011435113.1814364995
47.32269327842-0.911315465925-1.098381294245.02760746642-4.246276173843.94676668930.2056779318890.1064300125770.223723202433-0.615806574013-0.0878727228434-0.121498868498-0.173902381584-0.361571234729-0.1494137808590.52548717976-0.0840495063748-0.01951887421230.3856840941890.01330454455390.26158833453815.4323753583-8.6783372661725.0088531667
57.579913779956.1547730729-0.6121963138886.612817774282.026213601394.21252335476-0.417357060242-0.582922723721-0.704029262546-0.101723476683-0.1543308951640.03940900736270.348082864278-0.1271828158360.4020521367630.8470446468720.1767971827030.09150473131180.4568944413010.1754107302540.81078588210123.9263911119-23.289277095423.7788010532
62.3510159994-2.297676907122.256650708442.32334576041-2.452955026847.46589875652-0.0494145327185-1.77803560064-1.11508174950.995628889455-0.371406761365-0.94767301618-0.183001950280.9707739556140.3441763324250.910833214742-0.00534100109181-0.03510800514260.8927036833010.08694144167240.88066535033630.4750515218-11.418055527133.4215723585
70.3219235680320.2530249286461.164127141720.34214157110.9634452897924.29275104639-0.566069074956-0.157159915834-0.145715012047-0.600440160421-1.079559916711.38461568454-2.99713203838-0.00843750315791.827799975212.04322907656-0.160226438378-0.4427460214370.8716478534460.06227799599481.2065482614123.105503754-6.962870314216.16529228468
83.299636684770.404420697673-1.222209477855.75217623156-4.398914818013.86154051770.1455442713240.1312100509970.257995353755-0.2868515203580.0521180472696-0.1518000915160.180240788446-0.304956881753-0.181851569820.490938088636-0.0616220988499-0.03081755090050.309811955874-0.02655619194610.41227233746420.39175992251.6724198692315.3563477936
99.638422573793.40319356490.5388876926174.78939177304-1.66249478138.526412263310.3412546001950.02382836358460.228645364863-0.2396793207970.0478560967981-0.3420043951820.3006667137630.657639644315-0.3991748171070.439154530878-0.01138808981390.02742326608880.3821357621230.03749421371950.37744840856628.564025163217.6152145256.67941000417
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 57 through 83 )AA57 - 831 - 27
22chain 'A' and (resid 84 through 103 )AA84 - 10328 - 47
33chain 'A' and (resid 104 through 133 )AA104 - 13348 - 77
44chain 'A' and (resid 134 through 199 )AA134 - 19978 - 128
55chain 'A' and (resid 200 through 217 )AA200 - 217129 - 146
66chain 'A' and (resid 218 through 232 )AA218 - 232147 - 161
77chain 'B' and (resid 52 through 56 )BB52 - 561 - 5
88chain 'B' and (resid 57 through 91 )BB57 - 916 - 40
99chain 'B' and (resid 92 through 139 )BB92 - 13941 - 88

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