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

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Basic information

Entry
Database: PDB / ID: 6vek
TitleContact-dependent growth inhibition toxin-immunity protein complex from from E. coli 3006, full-length
Components
  • contact-dependent immunity protein CdiI
  • contact-dependent toxin CdiA
KeywordsTOXIN / 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 / homologyUncharacterized protein / :
Function and homology information
Biological speciesEscherichia coli 3006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.25 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) / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 4items
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
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 from E. coli 3006, full-length
Authors: Michalska, 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 ...Authors: Michalska, 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)
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.2Aug 18, 2021Group: Author supporting evidence / Database references / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_audit_support / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: contact-dependent toxin CdiA
I: contact-dependent immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)55,8312
Polymers55,8312
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-10 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.000, 71.769, 175.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein contact-dependent toxin CdiA / Contact-dependent inhibitor A


Mass: 36610.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 3006 (bacteria) / Plasmid: pMCSG58 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4T7DH52
#2: Protein contact-dependent immunity protein CdiI


Mass: 19220.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 3006 (bacteria) / Gene: BTQ06_14240 / Plasmid: pMCSG58 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A2C800
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% GLYCEROL ETHOXYLATE, 0.2 M AMMONIUM ACETATE, 0.1 M, MES PH 6.5

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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: Apr 3, 2016 / 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: 2.25→30 Å / Num. obs: 25933 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 25.4 % / Biso Wilson estimate: 47.52 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 30.3
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 17.2 % / Rmerge(I) obs: 1.242 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 1274 / CC1/2: 0.635 / CC star: 0.881 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXdev_2947refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: 6CP8

6cp8


Resolution: 2.25→29.256 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1652 6.5 %
Rwork0.1819 --
obs0.1852 25415 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.51 Å2 / Biso mean: 65.0312 Å2 / Biso min: 22.32 Å2
Refinement stepCycle: final / Resolution: 2.25→29.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 0 109 3765
Biso mean---51.3 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073735
X-RAY DIFFRACTIONf_angle_d0.7865046
X-RAY DIFFRACTIONf_dihedral_angle_d16.9092301
X-RAY DIFFRACTIONf_chiral_restr0.046564
X-RAY DIFFRACTIONf_plane_restr0.005663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.31620.35041470.26871937100
2.3162-2.39090.25751310.23311950100
2.3909-2.47630.30571270.21061943100
2.4763-2.57540.26881320.20811975100
2.5754-2.69260.28811310.21431936100
2.6926-2.83440.28621420.21261949100
2.8344-3.01180.29411510.21051958100
3.0118-3.24410.27041250.21611982100
3.2441-3.570.26751450.19071974100
3.57-4.08540.191460.16322004100
4.0854-5.14270.2181270.15132052100
5.1427-29.2560.18491480.1605210399
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)
12.0123-1.19660.15843.4996-0.02980.86310.06880.23850.0386-0.2131-0.09710.20440.0529-0.03530.01440.32970.00650.03980.33710.02080.3232-5.16196.1296-6.3013
22.05221.6734-0.40134.3669-2.15533.52490.1201-0.26570.14240.1269-0.10690.1039-0.0947-0.11470.01010.2450.02570.01910.2934-0.06430.3203-0.8927-7.55237.3967
31.5023-0.3413-0.30732.47832.19414.6648-0.0789-0.66340.07480.0420.0723-0.1154-0.15910.29320.03230.3827-0.0501-0.03510.61490.0470.3626-1.782-8.146527.3235
41.4226-0.4398-0.82270.13690.17223.2863-0.06580.0441-0.0311-0.1141-0.53291.2260.4133-1.70970.42710.6571-0.1009-0.16321.3105-0.52291.208-18.4662-3.806628.3422
58.79712.87810.93791.1279-0.84737.2412-0.21710.481-2.02790.2488-0.67181.49510.6762-1.84680.86060.6519-0.24420.00731.2622-0.43271.1949-18.7819-5.837739.881
63.7853-3.3924-1.47317.38364.55998.7257-0.5705-1.0006-0.17571.24630.39240.37570.91220.0210.20480.6714-0.05570.04950.9776-0.02680.5099-4.2964-1.899949.1038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 128 )A2 - 128
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 216 )A129 - 216
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 336 )A217 - 336
4X-RAY DIFFRACTION4chain 'I' and (resid 6 through 45 )I6 - 45
5X-RAY DIFFRACTION5chain 'I' and (resid 46 through 66 )I46 - 66
6X-RAY DIFFRACTION6chain 'I' and (resid 67 through 158 )I67 - 158

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