[English] 日本語
Yorodumi
- PDB-8ey4: Contact-dependent growth inhibition toxin-immunity protein comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ey4
TitleContact-dependent growth inhibition toxin-immunity protein complex from E. coli O32:H37
Components
  • Cys_rich_CPCC domain-containing protein
  • PT-VENN domain-containing protein
KeywordsTOXIN / CDI / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


primary metabolic process / macromolecule metabolic process / : / catalytic activity / toxin activity / cytoplasm
Similarity search - Function
Cysteine-rich CPCC domain / Cysteine-rich CPCC / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat
Similarity search - Domain/homology
: / Cysteine-rich CPCC domain-containing protein / VENN motif-containing domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli O32:H37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsMichalska, K. / Stols, L. / Eschenfeldt, W. / Goulding, C.W. / Hayes, C.S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Contact-dependent growth inhibition toxin-immunity protein complex from E. coli O32:H37
Authors: Michalska, K. / Stols, L. / Eschenfeldt, W. / Goulding, C.W. / Hayes, C.S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: Cys_rich_CPCC domain-containing protein
A: PT-VENN domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8713
Polymers17,8152
Non-polymers561
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-6 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.641, 53.660, 38.533
Angle α, β, γ (deg.)90.000, 102.550, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Cys_rich_CPCC domain-containing protein


Mass: 7635.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O32:H37 (bacteria)
Gene: B6R12_004683, B6R15_004523, C0P57_003609, D9E49_27105, DAH20_21150, DEN92_22940, DEN93_17480, DEO13_20945, DEO14_22190, DEO15_23150, E5S48_23695, E5S53_25065, E5S55_25155, FHQ91_23985, FJQ51_ ...Gene: B6R12_004683, B6R15_004523, C0P57_003609, D9E49_27105, DAH20_21150, DEN92_22940, DEN93_17480, DEO13_20945, DEO14_22190, DEO15_23150, E5S48_23695, E5S53_25065, E5S55_25155, FHQ91_23985, FJQ51_24360, FJQ53_24775, GF698_05830, GQW68_24765
Plasmid: pMCSG58 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y2XHL0
#2: Protein PT-VENN domain-containing protein


Mass: 10180.056 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O32:H37 (bacteria) / Gene: LH0189 / Plasmid: pMCSG58 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3ZTX4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25.7% PEG 5K MME, 150 mM MES pH 6.0, 6% propanediol, cryo 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 12331 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 25
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 565 / CC1/2: 0.895 / % possible all: 92

-
Processing

Software
NameVersionClassification
PHENIXdev_2947refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.83→28.71 Å / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 21.915 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.202 907 7.36 %
Rwork0.157 11418 -
obs0.161 12325 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.29 Å2
Refinement stepCycle: LAST / Resolution: 1.83→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 1 88 1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011187
X-RAY DIFFRACTIONf_angle_d11619
X-RAY DIFFRACTIONf_chiral_restr0.057158
X-RAY DIFFRACTIONf_plane_restr0.009222
X-RAY DIFFRACTIONf_dihedral_angle_d12.589708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.950.241450.191795X-RAY DIFFRACTION95.43
1.95-2.10.211480.161920X-RAY DIFFRACTION100
2.1-2.310.241570.161891X-RAY DIFFRACTION100
2.31-2.640.241710.161905X-RAY DIFFRACTION99.86
2.64-3.330.21420.161935X-RAY DIFFRACTION100
3.33-28.710.171440.141972X-RAY DIFFRACTION99.95
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)
10.59538731159-0.5014368361020.627955838244.451168109462.636191212793.14613615921-0.0524289994276-0.128978982029-0.02005370412860.320890305060.1037143958040.06749723105330.3638284927465.20450045367E-5-0.07291808787340.2350292383350.03181697543750.001650597832180.2648045382260.02718290794860.17773453945814.66368996294.6431118037731.1817120081
23.35704064554-0.114611815008-0.4320960436864.267880778242.100949285972.05049445376-0.229151216893-0.377501185408-0.447238673170.2830037469740.2296836885810.3615229841230.769885092189-0.6091145236270.01175253491950.242100646343-0.03303072390450.03075080263450.3172731570040.05100610826420.2780338758019.454558756071.9825472853428.4266078859
31.1860002378-0.190088207207-0.1593863888191.10783347488-0.06532342549671.266271447-0.142752095081-0.298986201041-0.0605345727360.1375598258760.120559827473-0.1110191607390.1134239935620.07203435048550.01375468877780.2080816236190.0354209054390.01108922624790.215483064623-0.009248951947590.20329060004614.61385414158.2076151899123.0890022361
43.81241866793-0.05043533042231.27449915122.94672825292-0.2229401470364.90331199984-0.2732338675390.05679817838380.1550730692530.2820095934810.0650583996116-0.456021039272-0.1166495742770.6161720765960.2409556796190.1885421478670.0100852536569-0.0155865839470.215644373076-0.01516219380920.24500207133723.060820933613.356158316119.7007369554
53.44401439204-0.0361331381819-5.104350044823.944648403411.823431890058.70576904061-0.231288734564-1.047428908770.8128441949830.7446683811680.0579147382838-0.468801431234-0.8677837610410.457265613912-0.07247548795240.3683212003480.0434843579957-0.1194108035770.420265013483-0.1146993558950.29587033543322.246845061916.12637147331.3483000775
63.223143092150.623999257435-0.5239399783351.933235723260.1188690149623.186079822730.0114625002473-0.3377312909020.2219643380240.0549283542706-0.1356824539430.0467919985926-0.377940126767-0.911274693912-0.03810353935810.182844919010.05902159258770.006453436181810.345431365932-0.07380625322460.2222922905783.8167903175415.996581889616.6693505901
75.51380901613-1.22680166505-3.868972694082.163683410021.96275647157.048030695310.187753411562-0.716550883571-0.04943989610290.337696280383-0.160347561119-0.09392112110690.614612323101-1.038836387660.04870647722870.195803307223-0.0393407924654-0.01509793521420.435370524419-0.03551559433190.2224176059421.5873488669911.45117703758.23167056545
81.414727740170.469333681032-0.8836029673951.47130852779-0.04302727401640.6630685228520.025335775078-0.00951926032239-0.2086126225650.053302560921-0.15915890371-0.3039328469330.0944975892143-0.0434731932120.1014926988740.236705653086-0.00311684304863-0.007412954338990.1461316019650.002386459701930.22420866237712.2059471782.603592551395.56579176834
91.75107937281-0.07716417842810.2248446151152.24334787772-0.8538375606612.683356766960.0362473144303-0.1007377181270.0594547177509-0.166450276004-0.01855656634410.2043773487690.0889717088204-0.182559591488-0.01744914029110.1706621609390.0031488755663-0.003862253544240.1430195305530.004521709907480.16682835529511.2457739958.839181594859.49993334356
104.59273897518-0.8218768918330.1799630462183.74592137660.9510751413975.138690303380.01323362292450.194063668242-0.21551280747-0.0361631538357-0.167466131249-0.3382675889140.5443964644770.832355509690.1927390978560.1899621992970.06860902591280.01802407725770.2050477003990.01749056061140.22336035594722.34353912188.313683378549.09871971631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'I' and (resid 5 through 14 )
2X-RAY DIFFRACTION2chain 'I' and (resid 15 through 19 )
3X-RAY DIFFRACTION3chain 'I' and (resid 20 through 39 )
4X-RAY DIFFRACTION4chain 'I' and (resid 40 through 51 )
5X-RAY DIFFRACTION5chain 'I' and (resid 52 through 62 )
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 80 )
7X-RAY DIFFRACTION7chain 'A' and (resid 81 through 93 )
8X-RAY DIFFRACTION8chain 'A' and (resid 94 through 108 )
9X-RAY DIFFRACTION9chain 'A' and (resid 109 through 136 )
10X-RAY DIFFRACTION10chain 'A' and (resid 137 through 144 )

+
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://pdbjlvh1.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