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- PDB-1a87: COLICIN N -

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Basic information

Entry
Database: PDB / ID: 1a87
TitleCOLICIN N
ComponentsCOLICIN N
KeywordsBACTERIOCIN / TOXIN / PORE-FORMING ACTIVITY
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / pore-forming activity / defense response to Gram-negative bacterium / killing of cells of another organism / transmembrane transporter binding / plasma membrane
Similarity search - Function
Colicin / Colicin / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / Arylsulfatase, C-terminal domain / Globin-like / 2-Layer Sandwich / Orthogonal Bundle ...Colicin / Colicin / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / Arylsulfatase, C-terminal domain / Globin-like / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å
AuthorsVetter, I.R. / Parker, M.W. / Tucker, A.D. / Lakey, J.H. / Pattus, F. / Tsernoglou, D.
Citation
Journal: Structure / Year: 1998
Title: Crystal structure of a colicin N fragment suggests a model for toxicity.
Authors: Vetter, I.R. / Parker, M.W. / Tucker, A.D. / Lakey, J.H. / Pattus, F. / Tsernoglou, D.
#1: Journal: Protein Toxin Structure / Year: 1996
Title: Insights Into Membrane Insertion Based on Studies of Colicins
Authors: Vetter, I.R. / Parker, M.W. / Pattus, F. / Tsernoglou, D.
#2: Journal: Eur.J.Biochem. / Year: 1993
Title: Characterization of the Receptor and Translocator Domains of Colicin N
Authors: El Kouhen, R. / Fierobe, H.P. / Scianimanico, S. / Steiert, M. / Pattus, F. / Pages, J.M.
#3: Journal: Eur.Biophys.J. / Year: 1990
Title: Colicin N Forms Voltage-and Ph-Dependent Channels in Planar Lipid Bilayer Membranes
Authors: Wilmsen, H.U. / Pugsley, A.P. / Pattus, F.
#4: Journal: Mol.Microbiol. / Year: 1990
Title: Involvement of Ompf During Reception and Translocation Steps of Colicin N Entry
Authors: Bourdineaud, J.P. / Fierobe, H.P. / Lazdunski, C. / Pages, J.M.
#5: Journal: Mol.Microbiol. / Year: 1987
Title: Nucleotide Sequencing of the Structural Gene for Colicin N Reveals Homology between the Catalytic, C-Terminal Domains of Colicins a and N
Authors: Pugsley, A.P.
History
DepositionApr 3, 1998Processing site: BNL
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLICIN N


Theoretical massNumber of molelcules
Total (without water)35,1461
Polymers35,1461
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.300, 187.300, 187.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein COLICIN N


Mass: 35146.270 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING AND PORE-FORMING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Variant: BZB 1019 / Plasmid: PCHAP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P08083
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.17 Å3/Da / Density % sol: 65 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMphosphate1reservoir
360 %(w/v)satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 3.1→22.7 Å / Num. obs: 10644 / % possible obs: 93.5 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.083 / Net I/σ(I): 33.07
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 6.3 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
GROPATmodel building
TNT5Erefinement
XDSdata reduction
XSCALEdata scaling
GROPATphasing
RefinementMethod to determine structure: MIR / Resolution: 3.1→23 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1037 10 %RANDOM
Rwork0.173 ---
all-10644 --
obs-10644 93.5 %-
Solvent computationBsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 3.1→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 0 55 2366
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0070.8
X-RAY DIFFRACTIONt_angle_deg1.41.5
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3
X-RAY DIFFRACTIONt_it34.61
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5EB / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg0
X-RAY DIFFRACTIONt_plane_restr3

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