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- PDB-2i88: Crystal structure of the Channel-forming Domain of Colicin E1 -

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Basic information

Entry
Database: PDB / ID: 2i88
TitleCrystal structure of the Channel-forming Domain of Colicin E1
ComponentsColicin-E1
KeywordsMEMBRANE PROTEIN / protein-membrane interactions / toxin-membrane interactions / toxin structure / voltage-gated channel / colicin
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / pore-forming activity / killing of cells of another organism / defense response to Gram-negative bacterium / transmembrane transporter binding / plasma membrane
Similarity search - Function
Colicin / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / Globin-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsElkins, P. / Bunker, A. / Cramer, W.A. / Stauffacher, C.V.
CitationJournal: Structure / Year: 1997
Title: A mechanism for toxin insertion into membranes is suggested by the crystal structure of the channel-forming domain of colicin E1
Authors: Elkins, P. / Bunker, A. / Cramer, W.A. / Stauffacher, C.V.
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_residues / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Colicin-E1


Theoretical massNumber of molelcules
Total (without water)21,1961
Polymers21,1961
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.46, 87.46, 59.10
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Colicin-E1


Mass: 21196.420 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DM1187 / Gene: cea / Plasmid: pSKHY / Production host: Escherichia coli (E. coli) / References: UniProt: P02978
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 50 mM MES at pH 6.0 25 mM Tris-HCl pH 7-8 100 mM NaCo or NaNO3 23-27% PEG 3350 very sensitive to temperatue stabilized by slow addition to of PEG 20,000 to 2-3%, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→32 Å / Num. all: 7727 / Num. obs: 6684 / % possible obs: 86.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 51.5 Å2 / Rsym value: 0.035 / Net I/σ(I): 13.97
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.5 / Num. unique all: 683 / % possible all: 61.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
DENZOdata reduction
CCP4(ROTAVATA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→32 Å / σ(F): 1 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 562 -random
Rwork0.172 ---
all0.182 7730 --
obs0.176 6684 86.5 %-
Displacement parametersBiso mean: 38.885 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 0 22 1414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.013

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