[English] 日本語
Yorodumi
- PDB-8yo6: Crystal structure of CagT from Helicobacter pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yo6
TitleCrystal structure of CagT from Helicobacter pylori
ComponentsCag 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 T
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,5092
Polymers27,5092
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical ultracentrifugation confirms the molecule exists in monomeric form, however, it exists as a dimer per asymmetric unit in the crystal.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-4 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.090, 86.250, 105.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 58 through 65 or resid 67...
d_2ens_1(chain "B" and (resid 58 through 65 or resid 67...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPVALVALAA58 - 6512 - 19
d_12LEULEUTYRTYRAA67 - 7021 - 24
d_13ASPASPVALVALAA72 - 8726 - 41
d_14HISHISGLYGLYAA89 - 11343 - 67
d_15SERSERLEULEUAA116 - 12670 - 80
d_16GLYGLYTYRTYRAA130 - 13884 - 92
d_21ASPASPVALVALBB58 - 6512 - 19
d_22LEULEUTYRTYRBB67 - 7021 - 24
d_23ASPASPVALVALBB72 - 8726 - 41
d_24HISHISGLYGLYBB89 - 11343 - 67
d_25SERSERLEULEUBB116 - 12670 - 80
d_26GLYGLYTYRTYRBB130 - 13884 - 92

NCS oper: (Code: givenMatrix: (0.936015393294, 0.282499594493, -0.209926564846), (0.278097721412, -0.959206651141, -0.0508355953342), (-0.215723992319, -0.0107971995875, -0.976394684346)Vector: -3. ...NCS oper: (Code: given
Matrix: (0.936015393294, 0.282499594493, -0.209926564846), (0.278097721412, -0.959206651141, -0.0508355953342), (-0.215723992319, -0.0107971995875, -0.976394684346)
Vector: -3.92812416621, 47.5839454473, 25.9027265091)

-
Components

#1: Protein Cag pathogenicity island protein T


Mass: 13754.686 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus III F1 condition 0.6% antibiotics mix, 0.1M buffer system 1, 30% v/v precipitant mix 1, 1% 1,4-dioxane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→33.83 Å / Num. obs: 17417 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1210 / CC1/2: 0.684 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.05 Å / SU ML: 0.1889 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 810 4.65 %
Rwork0.1919 16593 -
obs0.1937 17403 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 0 123 1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781370
X-RAY DIFFRACTIONf_angle_d0.86641850
X-RAY DIFFRACTIONf_chiral_restr0.0617208
X-RAY DIFFRACTIONf_plane_restr0.0064232
X-RAY DIFFRACTIONf_dihedral_angle_d4.5967176
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.978463879405 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.070.26981290.25142725X-RAY DIFFRACTION100
2.07-2.230.3031330.22832736X-RAY DIFFRACTION99.9
2.23-2.460.23211350.20452754X-RAY DIFFRACTION99.9
2.46-2.810.20571350.20132740X-RAY DIFFRACTION99.9
2.81-3.540.24331480.18862776X-RAY DIFFRACTION99.66
3.54-29.050.20121300.16592862X-RAY DIFFRACTION98.29
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)
13.387347554251.730745181192.452648780033.856317918181.160639849297.3286753499-0.0837891876646-0.1660857025850.00500317900430.44557081691-0.00455556919370.0900695913024-0.1135169824760.002326254569780.2777552990480.1483587549480.01900193438470.04253119664390.06950140144190.02832385963690.17938238546414.252890725228.41265222358.52460342275
26.495186194822.206195394281.017694559728.342567107514.523186800626.75115651057-0.0173380270010.227008671814-0.2106923214880.101418562373-0.1466211851650.6266716494170.223282575546-0.1949988390310.09074001355690.08546826326250.0259683176315-0.01764551416360.1617592128470.002383869202060.2423386032726.2377707070625.2214123804-0.455774924341
37.6426677867-1.58756410122-0.8082914141284.424073091390.9048965997293.86682740080.05492108157540.04616275630.244755564367-0.029659785182-0.01948604669020.229813749138-0.0841570267160.0247844453353-0.03987268175890.111193342609-0.006631540515640.003349906961020.08593979717180.03608009262430.16528229710613.450224846934.8294018554-2.32701503779
48.452403951-0.123543679039-3.916475740352.6995992851-2.013203906843.42851318463-0.2141356368590.305417923759-0.634821163663-0.06394472621-0.0821108745491-0.05861933254220.1284150488370.06896478792390.08212140194070.09596466391950.0052334532948-0.006821466234690.140346984873-0.004849581637520.18491561651919.560082105828.28318369740.25240002396
54.75182419729-2.39587537654-1.712556486972.20944769516-0.1652699742011.66729090092-0.07855694299050.272863660821-1.82044603334-0.350418175232-0.2751042703321.366376604942.36903349677-1.107938373730.1379782326370.482267529071-0.106947808988-0.020065181890.18905740506-0.02764238479880.56589909416512.624489888516.76768145125.29786708993
69.08711966517-1.27741253695-1.309082285388.331083981535.617799945847.430784311220.0904813213325-0.623150829580.2286225691311.148282726180.575975196415-0.4774753132820.484559666052-0.118576079481-0.5389192013910.302452173460.051643766157-1.02589283306E-50.2485080163460.1076602723650.22241954217417.754134860328.600895343819.7417198862
70.8143420393210.05400230574950.5364975380980.192725049623-0.288960553150.918667362840.0855130647793-0.6831538876770.1963934842710.450787926946-0.01003574745260.162787452585-0.66544930670.262633297739-0.420230508661.293797478890.2278671803210.5510123623820.669583655810.07851124054140.1103613154111.190137923329.108946700231.2728373433
87.36372368758-2.52497827242-6.115788453998.085747464940.2358801192038.36316106741-0.08784236753040.359828508646-0.2288999175130.3727521575180.5217593821182.01074345891-0.198532153039-1.44706939876-0.1727035998610.386375105353-0.01684703049170.1468081639670.4870101672390.2007588302420.469231129437.9416994334522.962569137920.5609986038
96.962481164994.078374151913.89104395294.542762961224.990574459565.679993059130.245144832515-0.562232274269-0.8131660664610.996311439064-0.0237748009114-0.736722156580.9362244766710.445907902927-0.3626207241730.4268022967410.052075686664-0.01093675474010.3191694671690.1498431734420.37403016706121.264900383620.140726164620.5940725076
104.242578084760.324824751027-1.203701096555.93933564249-0.5583023700883.64508120118-0.182031105153-1.12019692654-0.4153853998781.400039253460.1524189990640.001460679899730.4955144473610.2078874744440.01228115246520.6239589306770.00766820650949-0.03238164199680.6061210972170.2403403297140.27679213756917.997619368320.076599866630.0442300973
117.0511372835-0.908442783767-2.887824577941.103042069422.991544027828.132519011810.3091837375910.34434931596-0.7110524704410.91538308087-0.181121571343-0.1651838182671.2140718792-0.9682634428660.2481940635680.729082609035-0.1034186510030.1585705889380.5523254379660.3254207861740.88951719464212.996980546710.905758474922.5185080883
122.853458981450.8297730334782.714698818270.2344972009790.6999569131758.14925213158-0.2225235334610.3735161928190.406732492449-0.00587374539361-0.0214717577924-0.610603956291-0.2621061904130.8508433135170.169473421420.3876598229590.0812509652278-0.09060193977660.5061658899040.2258137319530.65370527129926.295063561424.057081046124.9088524972
137.438571505013.800871026233.900673214634.411424129325.199794090376.24851639086-0.127666758168-0.0866784532522-0.4699802631610.2897487470850.3162451172640.3036448226130.3903016713180.522764701935-0.104585958750.298743961421-0.00184782802519-0.0163763662810.196924620290.1003855304510.28563172349718.927243595521.516769951315.6363385227
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 69 )AA57 - 691 - 13
22chain 'A' and (resid 70 through 89 )AA70 - 8914 - 33
33chain 'A' and (resid 90 through 124 )AA90 - 12434 - 68
44chain 'A' and (resid 125 through 138 )AA125 - 13869 - 82
55chain 'B' and (resid 57 through 61 )BB57 - 611 - 5
66chain 'B' and (resid 62 through 69 )BB62 - 696 - 13
77chain 'B' and (resid 70 through 76 )BB70 - 7614 - 20
88chain 'B' and (resid 77 through 89 )BB77 - 8921 - 33
99chain 'B' and (resid 90 through 98 )BB90 - 9834 - 42
1010chain 'B' and (resid 99 through 111 )BB99 - 11143 - 55
1111chain 'B' and (resid 112 through 118 )BB112 - 11856 - 62
1212chain 'B' and (resid 119 through 130 )BB119 - 13063 - 74
1313chain 'B' and (resid 131 through 138 )BB131 - 13875 - 82

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more