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- PDB-1e44: ribonuclease domain of colicin E3 in complex with its immunity protein -

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Basic information

Entry
Database: PDB / ID: 1.0E+44
Titleribonuclease domain of colicin E3 in complex with its immunity protein
Components
  • COLICIN E3
  • IMMUNITY PROTEIN
KeywordsRIBONUCLEASE / INHIBITION / PROTEIN-PROTEIN INTERACTIONS / RIBOSOME INACTIVATION / TOXIN
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / tRNA binding ...negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / tRNA binding / rRNA binding / defense response to bacterium / lyase activity / extracellular region
Similarity search - Function
Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / Colicin, receptor domain ...Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Chitinase A; domain 3 / Roll / Alpha Beta
Similarity search - Domain/homology
Colicin E3 / Colicin E3 immunity protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCarr, S. / Walker, D. / James, R. / Kleanthous, C. / Hemmings, A.M.
CitationJournal: Structure / Year: 2000
Title: Inhibition of a Ribosome Inactivating Ribonuclease: The Crystal Structure of the Cytotoxic Domain of Colicin E3 in Complex with its Immunity Protein
Authors: Carr, S. / Walker, D. / James, R. / Kleanthous, C. / Hemmings, A.M.
History
DepositionJun 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNITY PROTEIN
B: COLICIN E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7853
Polymers20,7232
Non-polymers621
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-13.6 kcal/mol
Surface area10960 Å2
MethodPQS
Unit cell
Length a, b, c (Å)93.700, 93.700, 76.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein IMMUNITY PROTEIN


Mass: 9910.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02984
#2: Protein COLICIN E3


Mass: 10812.117 Da / Num. of mol.: 1 / Fragment: RIBONUCLEASE DOMAIN RESIDUES 456-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: CO-EXPRESSED WITH A HIS-TAGGED IMMUNITY PROTEIN
Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00646
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 4.39 Å3/Da / Density % sol: 72 %
Crystal growpH: 5.6
Details: 0.1 M NA CITRATE PH 5.6, 20% ISOPROPANOL, 10% PEG 4000
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Carr, S., (1999) Acta Crystallogr., D56, 1630.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
145-50 mg/mlprotein1drop
210 mMTris-HCl1drop
30.1 Msodium citrate1reservoir
420 %(v/v)PEG40001reservoir
520 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9, 0.97, 0.979
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.971
30.9791
ReflectionResolution: 2.4→20 Å / Num. obs: 14892 / % possible obs: 98.7 % / Redundancy: 3 % / Rsym value: 0.039 / Net I/σ(I): 37.8
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.237 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.237

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.228 726 5 %
Rwork0.192 --
obs0.192 14892 97.5 %
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 4 171 1633
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.86
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.45 Å / Rfactor Rfree: 0.229 / Rfactor obs: 0.194

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