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- PDB-1cii: COLICIN IA -

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Basic information

Entry
Database: PDB / ID: 1cii
TitleCOLICIN IA
ComponentsCOLICIN IA
KeywordsTRANSMEMBRANE PROTEIN / COLICIN / BACTERIOCIN / ION CHANNEL FORMATION
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 Ia; domain 1 / Colicin Ia, domain 1 / Colicin Ia; domain 2 / Colicin Ia; domain 2 / Channel forming colicin, N-terminal domain superfamily / Channel forming colicin, central receptor recognition / Colicin Ia / Colicin / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily ...Colicin Ia; domain 1 / Colicin Ia, domain 1 / Colicin Ia; domain 2 / Colicin Ia; domain 2 / Channel forming colicin, N-terminal domain superfamily / Channel forming colicin, central receptor recognition / Colicin Ia / Colicin / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / Globin-like / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsWiener, M. / Freymann, D. / Ghosh, P. / Stroud, R.
Citation
Journal: Nature / Year: 1997
Title: Crystal structure of colicin Ia.
Authors: Wiener, M. / Freymann, D. / Ghosh, P. / Stroud, R.M.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: The Domain Structure of the Ion Channel-Forming Protein Colicin Ia
Authors: Ghosh, P. / Mel, S.F. / Stroud, R.M.
#2: Journal: Thesis / Year: 1992
Title: The Structure and Function of Colicin Ia
Authors: Ghosh, P.
History
DepositionJan 8, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLICIN IA


Theoretical massNumber of molelcules
Total (without water)67,0361
Polymers67,0361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.400, 178.600, 285.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein COLICIN IA


Mass: 67036.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 294 / Gene: CIA / Plasmid: PJK5 / Gene (production host): CIA / Production host: Escherichia coli (E. coli) / Strain (production host): 294 / References: UniProt: P06716
Compound detailsTRANSLOCATION (T) DOMAIN: RESIDUES 23 - 225. RECEPTOR-BINDING (R) DOMAIN: RESIDUES 282 - 385. ...TRANSLOCATION (T) DOMAIN: RESIDUES 23 - 225. RECEPTOR-BINDING (R) DOMAIN: RESIDUES 282 - 385. CHANNEL (C) DOMAIN: RESIDUES 450 - 626. 160A LONG HELICES: RESIDUES 176 - 282 AND 359 - 467.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 5.9 Å3/Da / Density % sol: 78 %
Crystal growMethod: vapor diffusion - hanging drop - streak seeding / pH: 5.2
Details: PROTEIN WAS CRYSTALLIZED BY HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIRS OF 1.0 M NH4(SO4)2, 20 MM NA-CITRATE (PH 5.2), 200 MM NACL, STARTING WITH 6 MICROLITERS OF PROTEIN AT 2 MG/ML IN ...Details: PROTEIN WAS CRYSTALLIZED BY HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIRS OF 1.0 M NH4(SO4)2, 20 MM NA-CITRATE (PH 5.2), 200 MM NACL, STARTING WITH 6 MICROLITERS OF PROTEIN AT 2 MG/ML IN 20 MM NA-CITRATE (PH 5.2), 200 MM NACL, 5 MM DTT, AND 4 MICROLITERS RESERVOIR SOLUTION. THESE DROPS OF MUTANT PROTEIN WERE STREAK-SEEDED FROM STOCKS GENERATED FROM CRUSHED DIFFRACTION-QUALITY WILD-TYPE COLICIN IA CRYSTALS. CRYSTALS WERE HARVESTED TO 1.1 M NA2SO4, 200 MM NACL, 20 MM NA-CITRATE (PH 5.2), AND 5 MM DTT. FOR DERIVATIZATION, CRYSTALS WERE WASHED IN DTT-FREE HARVEST BUFFER AND SOAKED FOR ONE WEEK IN 1 MM CH3HGCL., vapor diffusion - hanging drop - streak seeding
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlprotein1drop
220 mMNa-citrate1drop
3200 mM1dropNaCl
45 mMdithiothreitol1drop
51.0 Mammonium sulfate1reservoir
620 mMsodium citrate1reservoir
7200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1994 / Details: PT-COATED FUSED SILICA MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 28266 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 5.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.309 / % possible all: 73
Reflection shell
*PLUS
% possible obs: 73 %

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Processing

Software
NameVersionClassification
PHASESphasing
SOLOMONphasing
X-PLOR3.1model building
XTALVIEWrefinement
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 3→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: ANISOTROPIC B-FACTOR CORRECTION APPLIED TO THE DIFFRACTION DATA. BULK SOLVENT MASK CALCULATED AND UTILIZED.
RfactorNum. reflection% reflectionSelection details
Rfree0.312 2000 7.1 %RANDOM
Rwork0.241 ---
obs0.241 28260 84.1 %-
Displacement parametersBiso mean: 66.5 Å2
Refine analyzeLuzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 0 0 4714
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.34
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.53
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it22.5
LS refinement shellResolution: 3→3.1 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.392 169 8 %
Rwork0.373 2117 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.34
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.53

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