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- PDB-8ey4: Contact-dependent growth inhibition toxin-immunity protein comple... -

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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


catalytic activity / toxin activity / metal ion binding / cytoplasm
Similarity search - Function
Cysteine-rich CPCC domain / Cysteine-rich CPCC / Filamentous haemagglutinin repeat / Haemagglutinin repeat / 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
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: 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

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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

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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 )

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