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- PDB-6cp8: Contact-dependent growth inhibition toxin-immunity protein comple... -

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Basic information

Entry
Database: PDB / ID: 6cp8
TitleContact-dependent growth inhibition toxin-immunity protein complex from from E. coli 3006
Components
  • CdiA
  • CdiI
KeywordsTOXIN/ANTITOXIN / toxin / RNase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI / TOXIN-ANTITOXIN complex
Function / homologyVENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / : / toxin activity / cytoplasm / Tetratricopeptide repeat protein / Toxin CdiA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.201 Å
AuthorsMichalska, K. / Stols, L. / Eschenfeldt, W. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102318 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
Citation
Journal: Structure / Year: 2019
Title: Convergent Evolution of the Barnase/EndoU/Colicin/RelE (BECR) Fold in Antibacterial tRNase Toxins.
Authors: Gucinski, G.C. / Michalska, K. / Garza-Sanchez, F. / Eschenfeldt, W.H. / Stols, L. / Nguyen, J.Y. / Goulding, C.W. / Joachimiak, A. / Hayes, C.S.
#1: Journal: Proteins / Year: 2019
Title: Target highlights in CASP13: Experimental target structures through the eyes of their authors.
Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / ...Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / Goulding, C.W. / Gurusaran, M. / Gutsche, I. / Harding, C.J. / Hartmann, M.D. / Hayes, C.S. / Joachimiak, A. / Leiman, P.G. / Loppnau, P. / Lovering, A.L. / Lunin, V.V. / Michalska, K. / Mir-Sanchis, I. / Mitra, A. / Moult, J. / Phillips Jr., G.N. / Pinkas, D.M. / Rice, P.A. / Tong, Y. / Topf, M. / Walton, J.D. / Schwede, T.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Nov 20, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CdiA
B: CdiA
C: CdiI
D: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9367
Polymers73,5144
Non-polymers4223
Water3,135174
1
A: CdiA
C: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0874
Polymers36,7572
Non-polymers3302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-11 kcal/mol
Surface area14480 Å2
MethodPISA
2
B: CdiA
D: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8493
Polymers36,7572
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-5 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.707, 106.534, 72.654
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CdiA / Contact-dependent inhibitor A


Mass: 17999.445 Da / Num. of mol.: 2 / Mutation: deltaN332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BTQ06_14245 / Variant: O157:H16 / Plasmid: pMCSG63 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2A2CAY5
#2: Protein CdiI


Mass: 18757.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BTQ06_14240 / Variant: O157:H16 / Plasmid: pMCSG63 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2A2C800
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES/Na pH 7.0, 18% PEG12K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2014 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 38085 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.28
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 1879 / CC1/2: 0.664 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.201→29.632 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 1189 3.12 %
Rwork0.1761 --
obs0.1774 38054 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.201→29.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5011 0 27 174 5212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075136
X-RAY DIFFRACTIONf_angle_d0.8236935
X-RAY DIFFRACTIONf_dihedral_angle_d14.2863138
X-RAY DIFFRACTIONf_chiral_restr0.047761
X-RAY DIFFRACTIONf_plane_restr0.005908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2008-2.3010.29551370.23434354X-RAY DIFFRACTION93
2.301-2.42220.26591350.22334639X-RAY DIFFRACTION100
2.4222-2.57390.27691520.21854608X-RAY DIFFRACTION100
2.5739-2.77250.24721560.21494652X-RAY DIFFRACTION100
2.7725-3.05120.26691560.20734615X-RAY DIFFRACTION100
3.0512-3.49220.24311360.19224665X-RAY DIFFRACTION100
3.4922-4.39740.17691550.14574648X-RAY DIFFRACTION100
4.3974-29.63430.17681620.14064684X-RAY DIFFRACTION99
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)
13.635-1.58151.88957.91470.42154.6812-0.11530.47990.6315-0.36530.1606-0.465-0.5060.12010.03460.3063-0.05680.03360.3792-0.03370.3582-4.207411.842572.1758
22.371-0.61152.91976.55340.15793.8427-0.2834-0.05680.71220.02190.17370.185-0.14-0.2062-0.01140.36530.09090.01770.35790.00830.3256-13.66059.55274.097
34.79480.77374.18232.9445-0.42354.25780.27771.301-0.09810.1648-0.19120.80250.16871.5730.32970.62420.1166-0.00770.5217-0.02610.4303-23.567511.987276.1192
43.23331.7364.46541.39361.94446.845-0.1737-0.4310.6971-0.2933-0.43950.2814-0.453-0.63230.42250.30370.1476-0.01520.3489-0.03960.4296-40.06679.954462.9969
52.1566-0.4293-0.34940.1978-0.43453.8229-0.15380.46860.35620.4377-0.02380.505-0.4241-0.77090.03680.3490.0384-0.05190.4787-0.05880.4126-42.31695.141349.2461
62.1136-0.26593.41060.3949-0.29967.81550.16560.0174-0.03530.0440.14210.08420.0313-0.0511-0.0390.28660.03070.03590.248-0.00610.29-28.20076.962571.2266
76.6169-4.8035-7.26476.53157.23789.2964-0.09610.2391-0.31140.0553-0.24970.36780.1818-0.0580.40670.3344-0.049-0.00320.39520.01410.3482-11.24616.705784.7631
85.17890.7141-3.46172.94981.13777.49490.18740.3544-0.53340.27080.5088-0.41121.51840.26450.03680.48780.0685-0.090.3356-0.01550.4253-7.3799-4.049672.8505
93.65530.3118-4.03541.1989-0.94295.5722-0.06840.0828-0.31210.1608-0.00180.01760.0916-0.1264-0.09730.31510.0074-0.01230.29210.0230.2805-15.8473-2.686779.8233
105.25981.376-4.71891.6731-1.75295.3265-0.0430.3032-0.14690.07930.2711-0.128-0.0536-0.2251-0.27570.33080.0194-0.00360.3214-0.06440.2537-12.43520.449969.2926
113.18821.86081.64073.49770.6158.2694-0.094-0.3832-0.17190.0040.11430.92410.3096-0.3795-0.01180.31670.1204-0.04940.44910.14060.4813-28.0749-41.385657.0929
122.90780.89430.20234.1195-0.33143.30150.02760.00120.1027-0.2784-0.0532-0.09710.3385-0.17490.00790.39160.023-0.06260.38220.06580.3417-23.4485-38.124849.7541
136.0435-0.1708-4.0894.3154-1.52894.6259-0.16070.6129-0.2903-0.7429-0.5608-0.64010.696-0.31290.35980.54310.09890.06290.39020.08950.5152-10.0088-31.604349.7861
141.77851.1709-2.04262.7939-3.21397.4233-0.1438-0.1386-0.4391-0.5603-0.2579-0.41570.70370.53240.48520.57850.14030.13220.38090.03980.518-3.6558-23.957327.1843
151.59040.5255-1.37772.1278-1.80612.1571-0.0991-0.042-0.2269-0.2808-0.2423-0.4625-0.00290.65890.25860.35440.04360.0170.290.09640.4794-10.2919-25.365741.3946
162.48321.2326-0.67142.8241-3.26544.05640.0404-0.1054-0.58210.3458-0.0751-0.44020.30660.12780.19460.485-0.001-0.06690.41040.05310.4238-16.9742-30.929262.3541
174.56950.27434.35584.4720.39954.1471-0.0983-0.01130.10740.25870.11450.3799-0.4026-0.3986-0.17850.32610.0208-0.00190.36730.04370.3522-31.9904-25.682252.7932
189.07170.95995.90833.43781.52969.2454-0.02950.19540.2908-0.06540.1878-0.297-0.6330.1453-0.16230.37170.02450.03880.281-0.0050.2695-25.0418-24.148752.4805
197.2729-0.79093.7072.7819-0.97387.70930.12980.70720.55210.2613-0.256-0.3817-1.18270.6926-0.0240.3866-0.01160.06860.3792-0.03590.3858-15.2345.455250.5611
207.1631-0.08042.98292.69522.0387.46990.0204-0.15180.3666-0.2030.3018-0.3081-0.67820.9526-0.03140.3557-0.10490.04360.336-0.03330.3117-11.5567.449361.0758
216.19180.14213.7922.1399-0.20388.4513-0.10970.13750.7858-0.0718-0.10320.1576-0.8766-0.01410.17240.3573-0.00510.02930.25720.00110.3453-22.97877.206954.1888
226.37940.13843.10331.8975-0.42187.78620.46140.5238-0.0445-0.2735-0.11420.0744-0.32260.2587-0.33810.29120.08190.01550.349-0.0550.3011-23.9155-1.919147.2359
235.4668-0.5028-0.0824.56022.79716.87060.06-0.4812-0.00530.02850.3337-0.46160.46251.2579-0.10480.49270.04720.00830.33440.00160.3994-18.154-6.872559.666
246.78990.49031.43513.76160.63185.3454-0.06960.20630.401-0.3974-0.25430.4084-0.4589-0.25440.07820.25840.0114-0.02260.3107-0.01340.2903-31.109-1.657952.7215
255.51690.16130.94533.14290.39444.83750.020.4316-0.3418-0.45360.10620.00690.6564-0.2445-0.07970.30650.00770.01420.2799-0.05260.274-32.2585-12.434853.0252
264.33850.1710.32063.31410.52324.10980.34150.3187-0.1804-0.3293-0.20910.21830.1682-0.48490.11040.27620.0053-0.04750.336-0.06440.2943-42.018-6.434955.3188
275.76711.7564.76350.62341.63067.06440.3638-0.249-1.37460.2123-0.00360.08061.6725-0.7567-0.28320.5172-0.137-0.05770.3973-0.00890.4758-37.9534-15.858363.4193
282.1212-0.21882.6434.19240.66216.85730.3569-0.22550.3837-0.0095-0.28980.14280.0934-0.24320.08310.3313-0.06070.02980.3591-0.00820.3633-32.1005-5.553772.3684
292.3336-0.16063.33113.36230.21947.33330.2083-0.56020.23070.3176-0.42780.6676-0.6651-0.7339-0.01240.28310.00020.00080.49240.08930.3917-44.0427-6.59366.8779
303.1626-4.53010.38566.5339-1.11676.6235-0.09680.0001-0.1751-0.0847-0.13512.17651.1149-2.1145-0.67260.5368-0.2963-0.07990.60050.07250.7284-50.504-13.384661.651
316.84370.5462-2.87514.81972.43299.3653-0.68270.5252-1.1716-0.17030.03510.13660.97250.09970.39860.5547-0.09490.00010.3288-0.00240.5008-29.3971-31.656128.714
323.81231.9317-0.09544.4899-0.67082.2214-0.2119-0.0616-0.5779-0.31950.0925-0.24320.8948-0.03190.10920.6303-0.05360.00480.316-0.00730.4164-23.3317-31.890633.5369
334.40041.3552-0.92294.7946-0.37442.3466-0.66080.81480.2202-0.69790.68670.21170.7972-0.65840.02160.6333-0.2034-0.1020.44630.04640.3887-25.9345-21.865423.5089
343.60062.1279-0.8634.4012-0.87223.514-0.18680.25350.1611-0.35980.23690.12760.1849-0.3226-0.03360.41920.0057-0.05290.2441-0.00540.2461-21.0875-18.89629.4575
354.11462.1798-0.60343.7318-1.51134.9815-0.00590.11330.1488-0.35070.10450.16280.30980.0652-0.0950.3606-0.0208-0.0290.19920.01890.2438-15.0302-10.314127.6772
362.47130.2272-0.18582.0958-0.79463.10990.12030.0807-0.0364-0.22270.04850.07510.08920.0219-0.12770.3286-0.0020.02330.2109-0.01570.2872-11.9881-6.944532.642
375.2151.0675-1.20353.8076-3.11643.64810.310.04240.3323-0.2282-0.6933-0.845-0.17741.33330.07320.3439-0.01540.04160.39210.01270.3213-3.294-5.043432.0575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 175 through 197 )
2X-RAY DIFFRACTION2chain 'A' and (resid 198 through 208 )
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 216 )
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 233 )
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 241 )
6X-RAY DIFFRACTION6chain 'A' and (resid 242 through 276 )
7X-RAY DIFFRACTION7chain 'A' and (resid 277 through 285 )
8X-RAY DIFFRACTION8chain 'A' and (resid 286 through 299 )
9X-RAY DIFFRACTION9chain 'A' and (resid 300 through 320 )
10X-RAY DIFFRACTION10chain 'A' and (resid 321 through 336 )
11X-RAY DIFFRACTION11chain 'B' and (resid 175 through 183 )
12X-RAY DIFFRACTION12chain 'B' and (resid 184 through 208 )
13X-RAY DIFFRACTION13chain 'B' and (resid 209 through 216 )
14X-RAY DIFFRACTION14chain 'B' and (resid 217 through 241 )
15X-RAY DIFFRACTION15chain 'B' and (resid 242 through 270 )
16X-RAY DIFFRACTION16chain 'B' and (resid 271 through 285 )
17X-RAY DIFFRACTION17chain 'B' and (resid 286 through 299 )
18X-RAY DIFFRACTION18chain 'B' and (resid 300 through 336 )
19X-RAY DIFFRACTION19chain 'C' and (resid 4 through 20 )
20X-RAY DIFFRACTION20chain 'C' and (resid 21 through 30 )
21X-RAY DIFFRACTION21chain 'C' and (resid 31 through 45 )
22X-RAY DIFFRACTION22chain 'C' and (resid 46 through 59 )
23X-RAY DIFFRACTION23chain 'C' and (resid 60 through 66 )
24X-RAY DIFFRACTION24chain 'C' and (resid 67 through 81 )
25X-RAY DIFFRACTION25chain 'C' and (resid 82 through 97 )
26X-RAY DIFFRACTION26chain 'C' and (resid 98 through 123 )
27X-RAY DIFFRACTION27chain 'C' and (resid 124 through 135 )
28X-RAY DIFFRACTION28chain 'C' and (resid 136 through 145 )
29X-RAY DIFFRACTION29chain 'C' and (resid 146 through 156 )
30X-RAY DIFFRACTION30chain 'C' and (resid 157 through 161 )
31X-RAY DIFFRACTION31chain 'D' and (resid 5 through 20 )
32X-RAY DIFFRACTION32chain 'D' and (resid 21 through 45 )
33X-RAY DIFFRACTION33chain 'D' and (resid 46 through 59 )
34X-RAY DIFFRACTION34chain 'D' and (resid 60 through 81 )
35X-RAY DIFFRACTION35chain 'D' and (resid 82 through 113 )
36X-RAY DIFFRACTION36chain 'D' and (resid 114 through 145 )
37X-RAY DIFFRACTION37chain 'D' and (resid 146 through 161 )

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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

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