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- PDB-5j4a: CdiA-CT toxin from Burkholderia pseudomallei E479 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5j4a
TitleCdiA-CT toxin from Burkholderia pseudomallei E479 in complex with cognate CdiI immunity protein
Components
  • Immunity protein CdiI
  • tRNA nuclease CdiA
KeywordsTOXIN / complex / endonuclease / immunity protein
Function / homology
Function and homology information


toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / tRNA binding
Similarity search - Function
CdiA, C-terminal tRNase domain / CdiA C-terminal tRNase domain / Hemagglutinin repeat / Hemagglutinin repeat
Similarity search - Domain/homology
tRNA nuclease CdiA / Immunity protein CdiI
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsGoulding, C.W. / Johnson, P.M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei.
Authors: Johnson, P.M. / Gucinski, G.C. / Garza-Sanchez, F. / Wong, T. / Hung, L.W. / Hayes, C.S. / Goulding, C.W.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA nuclease CdiA
B: Immunity protein CdiI
C: tRNA nuclease CdiA
D: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)60,7584
Polymers60,7584
Non-polymers00
Water2,792155
1
A: tRNA nuclease CdiA
B: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)30,3792
Polymers30,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-5 kcal/mol
Surface area10430 Å2
MethodPISA
2
C: tRNA nuclease CdiA
D: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)30,3792
Polymers30,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-5 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.472, 73.260, 110.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-246-

HOH

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Components

#1: Protein tRNA nuclease CdiA / Toxin CdiA


Mass: 16841.900 Da / Num. of mol.: 2 / Mutation: D285A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: cdiA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: H9T8G6, Hydrolases; Acting on ester bonds
#2: Protein Immunity protein CdiI


Mass: 13537.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: cdiI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9T8G7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.8 Å3/Da / Density % sol: 31.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.98
Details: 0.1 M HEPES (pH 6.98), 0.02 M magnesium chloride, 30% (w/v) polyacrylic acid

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97591 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97591 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30121 / % possible obs: 99.24 % / Redundancy: 10.7 % / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIXphenix.refine (1.8.2_1309)refinement
HKL-2000data collection
PHENIXPhaser-MR: 1.10.1-2155phasing
PHENIXAutoBuild: 1.10.1_2155model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→43.713 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2366 1999 6.64 %
Rwork0.1931 --
obs0.196 30094 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.004→43.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 0 155 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083442
X-RAY DIFFRACTIONf_angle_d1.0944654
X-RAY DIFFRACTIONf_dihedral_angle_d13.1471260
X-RAY DIFFRACTIONf_chiral_restr0.073526
X-RAY DIFFRACTIONf_plane_restr0.005610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0041-2.05420.28411290.24481822X-RAY DIFFRACTION91
2.0542-2.10980.28851420.23531998X-RAY DIFFRACTION100
2.1098-2.17190.25161420.22231986X-RAY DIFFRACTION100
2.1719-2.2420.27371410.21461983X-RAY DIFFRACTION100
2.242-2.32210.29591410.20431982X-RAY DIFFRACTION100
2.3221-2.41510.27511430.20692009X-RAY DIFFRACTION100
2.4151-2.5250.2351420.21172006X-RAY DIFFRACTION100
2.525-2.65810.25671420.20971988X-RAY DIFFRACTION100
2.6581-2.82460.28041420.21062009X-RAY DIFFRACTION100
2.8246-3.04260.26171460.21632040X-RAY DIFFRACTION100
3.0426-3.34870.23491440.20652016X-RAY DIFFRACTION100
3.3487-3.8330.23261440.18452040X-RAY DIFFRACTION100
3.833-4.82820.21471470.16952060X-RAY DIFFRACTION100
4.8282-43.72310.20351540.17312156X-RAY DIFFRACTION99

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