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- PDB-1col: REFINED STRUCTURE OF THE PORE-FORMING DOMAIN OF COLICIN A AT 2.4 ... -

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Entry
Database: PDB / ID: 1col
TitleREFINED STRUCTURE OF THE PORE-FORMING DOMAIN OF COLICIN A AT 2.4 ANGSTROMS RESOLUTION
ComponentsCOLICIN A
KeywordsANTIBACTERIAL PROTEIN
Function / homology
Function and homology information


pore-forming activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / Resolution: 2.4 Å
AuthorsParker, M.W. / Postma, J.P.M. / Pattus, F. / Tucker, A.D. / Tsernoglou, D.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined structure of the pore-forming domain of colicin A at 2.4 A resolution.
Authors: Parker, M.W. / Postma, J.P. / Pattus, F. / Tucker, A.D. / Tsernoglou, D.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Fluorescence Energy Transfer Distance Measurements Using Site-Directed Single Cysteine Mutants
Authors: Lakey, J.H. / Baty, D. / Pattus, F.
#2: Journal: Experientia / Year: 1990
Title: Colicins: Prokaryotic Killer-Pores
Authors: Pattus, F. / Massotte, D. / Wilmsen, H.U. / Lakey, J. / Tsernoglou, D. / Tucker, A. / Parker, M.W.
#3: Journal: Nature / Year: 1989
Title: Structure of the Membrane-Pore-Forming Fragment of Colicin A
Authors: Parker, M.W. / Pattus, F. / Tucker, A.D. / Tsernoglou, D.
#4: Journal: Biochim.Biophys.Acta / Year: 1988
Title: The Membrane Channel-Forming Colicin A: Synthesis, Secretion, Structure, Action and Immunity
Authors: Lazdunski, C.J. / Baty, D. / Geli, V. / Cavard, D. / Morlon, J. / Howard, R.Lloubes.S.P. / Knibiehler, M. / Chartier, M. / Varenne, S. / Frenette, M. / Dasseux, J.-L. / Pattus, F.
#5: Journal: Eur.Biophys.J. / Year: 1987
Title: Gating Processes of Channels Induced by Colicin A, its C-Terminal Fragment and Colicin E1 in Planar Lipid Bilayers
Authors: Collarini, M. / Amblard, G. / Lazdunski, C. / Pattus, F.
#6: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallization of the C-Terminal Domain of Colicin A Carrying the Voltage-Dependent Pore Activity of the Protein
Authors: Tucker, A.D. / Pattus, F. / Tsernoglou, D.
History
DepositionJul 6, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: 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 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COLICIN A
B: COLICIN A


Theoretical massNumber of molelcules
Total (without water)43,6362
Polymers43,6362
Non-polymers00
Water1,49583
1
A: COLICIN A


Theoretical massNumber of molelcules
Total (without water)21,8181
Polymers21,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: COLICIN A


Theoretical massNumber of molelcules
Total (without water)21,8181
Polymers21,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.000, 73.000, 171.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.47345, -0.01458, 0.88043), (0.02549, -0.99942, -0.03027), (0.88018, 0.03679, -0.47323)
Vector: -8.972, 90.1, 15.452)

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Components

#1: Protein COLICIN A


Mass: 21818.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: Q47108
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 190.133-134 1986
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1dropg
250 mMcitrate1dropcan be replaced with succinate
32.3 Mammonium sulfate1drop
450 mMcitrate1reservoircan be replaced with succinate
52.3 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Num. obs: 10024 / Observed criterion σ(F): 3 / Rmerge F obs: 0.244

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→6 Å / Rfactor obs: 0.18
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 0 83 3041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.82
X-RAY DIFFRACTIONp_mcangle_it2.93
X-RAY DIFFRACTIONp_scbond_it5.94.5
X-RAY DIFFRACTIONp_scangle_it8.46
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1570.15
X-RAY DIFFRACTIONp_singtor_nbd0.2440.5
X-RAY DIFFRACTIONp_multtor_nbd0.3740.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1980.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor22.115
X-RAY DIFFRACTIONp_orthonormal_tor31.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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