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- PDB-4g6u: CdiA-CT/CdiI toxin and immunity complex from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 4g6u
TitleCdiA-CT/CdiI toxin and immunity complex from Escherichia coli
Components
  • EC869 CdiA-CT
  • EC869 CdiI
KeywordsTOXIN / Beta-augmentation / DNase / immunity
Function / homology
Function and homology information


deoxyribonuclease I activity / : / toxin activity / cytoplasm
Similarity search - Function
Helix Hairpins - #1810 / Trna Endonuclease; Chain: A, domain 1 - #110 / CDI toxin, EC869-like / Immunity protein CdiI, Proteobacteria type / Immunity protein Cdil-like superfamily / CDI immunity protein / NMB0488-like fold / NMB0488-like / VENN motif-containing domain / Pre-toxin domain with VENN motif ...Helix Hairpins - #1810 / Trna Endonuclease; Chain: A, domain 1 - #110 / CDI toxin, EC869-like / Immunity protein CdiI, Proteobacteria type / Immunity protein Cdil-like superfamily / CDI immunity protein / NMB0488-like fold / NMB0488-like / VENN motif-containing domain / Pre-toxin domain with VENN motif / Trna Endonuclease; Chain: A, domain 1 / Helix Hairpins / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / YTTRIUM (III) ION / Toxin CdiA / DUF1436 family protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.353 Å
AuthorsMorse, R.P. / Nikolakakis, K. / Willet, J. / Gerrick, E. / Low, D.A. / Hayes, C.S. / Goulding, C.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems.
Authors: Morse, R.P. / Nikolakakis, K.C. / Willett, J.L. / Gerrick, E. / Low, D.A. / Hayes, C.S. / Goulding, C.W.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EC869 CdiA-CT
B: EC869 CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,66810
Polymers53,1242
Non-polymers5458
Water1,38777
1
A: EC869 CdiA-CT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7983
Polymers32,6971
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EC869 CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8707
Polymers20,4261
Non-polymers4446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-8 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.699, 103.631, 125.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein EC869 CdiA-CT


Mass: 32697.205 Da / Num. of mol.: 1 / Fragment: UNP residues 88-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: O157:H7 / Production host: Escherichia coli (E. coli) / References: UniProt: F2WK69
#2: Protein EC869 CdiI


Mass: 20426.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: O157:H7 / Production host: Escherichia coli (E. coli) / References: UniProt: F2WK70

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Non-polymers , 5 types, 85 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Y
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium acetate pH 5.5, 0.2 M NaCl. 18% PEG-6000, 10 mM yttrium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→39.9 Å / Num. obs: 22419 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.3 %
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 14.6 % / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
FRODOmodel building
CRANK2phasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.353→39.9 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1145 5.13 %RANDOM
Rwork0.1804 ---
obs0.1828 22333 99.72 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.15 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.8324 Å2-0 Å2-0 Å2
2---3.9227 Å2-0 Å2
3----8.9097 Å2
Refinement stepCycle: LAST / Resolution: 2.353→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 17 77 3010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082982
X-RAY DIFFRACTIONf_angle_d1.0794038
X-RAY DIFFRACTIONf_dihedral_angle_d13.9221085
X-RAY DIFFRACTIONf_chiral_restr0.075454
X-RAY DIFFRACTIONf_plane_restr0.004519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3531-2.46020.26971610.2162582X-RAY DIFFRACTION100
2.4602-2.58990.28361440.22012600X-RAY DIFFRACTION100
2.5899-2.75210.27931460.21632639X-RAY DIFFRACTION100
2.7521-2.96450.30961430.21212614X-RAY DIFFRACTION100
2.9645-3.26280.26661350.19892656X-RAY DIFFRACTION100
3.2628-3.73460.21141470.17832650X-RAY DIFFRACTION100
3.7346-4.7040.17771310.14842701X-RAY DIFFRACTION100
4.704-39.91790.20541380.16562746X-RAY DIFFRACTION98
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)
10.5182-0.5243-0.02867.57191.71420.71830.11440.13510.225-0.0622-0.0901-0.4452-0.1835-0.0536-0.04070.42110.13330.0170.31080.0370.3377-15.745960.611834.3988
22.16442.3342-4.54446.14342.2423.809-0.4287-0.8545-0.76390.7611-0.0144-0.36690.5411-0.26410.33850.58710.0670.01340.35780.04740.3095-15.136226.49645.1703
36.5045-1.29321.01941.0636-0.1431.5324-0.3686-0.37550.56910.36970.1724-0.0258-0.1706-0.17110.17910.41010.0901-0.04390.2198-0.0470.2539-5.053339.246144.4927
46.55050.71393.84943.21151.35417.76970.04150.0676-0.02150.1411-0.1482-0.2044-0.01830.47540.07960.23820.01860.01820.16890.02980.229623.464628.77347.5164
55.7419-1.24975.03080.8352-1.56344.5773-0.19380.4847-0.5392-0.70110.6023-0.09710.753-0.8375-0.27630.7167-0.21470.01520.81770.03630.311416.735121.267962.4319
67.6940.1389-0.8665.27071.1865.4675-0.0456-0.64490.55320.2354-0.0328-0.0334-0.9516-0.37350.10770.39190.0569-0.13390.3421-0.03920.26317.251638.561353.584
78.4671-5.799-0.63316.34410.58637.67720.0616-0.29381.1431-0.5157-0.0399-0.1102-1.24580.5517-0.02590.7035-0.186-0.13220.3633-0.02280.518628.068443.632552.9701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 85:156 )A85 - 156
2X-RAY DIFFRACTION2( CHAIN A AND RESID 157:178 )A157 - 178
3X-RAY DIFFRACTION3( CHAIN A AND RESID 179:292 )A179 - 292
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:76 )B2 - 76
5X-RAY DIFFRACTION5( CHAIN B AND ( RESID 77:106 OR RESID 107:107 ) )B77 - 106
6X-RAY DIFFRACTION5( CHAIN B AND ( RESID 77:106 OR RESID 107:107 ) )B107
7X-RAY DIFFRACTION6( CHAIN B AND RESID 108:138 )B108 - 138
8X-RAY DIFFRACTION7( CHAIN B AND RESID 139:164 )B139 - 164

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