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- PDB-1cei: STRUCTURE DETERMINATION OF THE COLICIN E7 IMMUNITY PROTEIN (IMME7... -

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Basic information

Entry
Database: PDB / ID: 1cei
TitleSTRUCTURE DETERMINATION OF THE COLICIN E7 IMMUNITY PROTEIN (IMME7) THAT BINDS SPECIFICALLY TO THE DNASE-TYPE COLICIN E7 AND INHIBITS ITS BACTERIOCIDAL ACTIVITY
ComponentsCOLICIN E7 IMMUNITY PROTEIN
KeywordsANTIBACTERIAL PROTEIN / IMMUNITY PROTEIN
Function / homology
Function and homology information


bacteriocin immunity / toxic substance binding
Similarity search - Function
Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Colicin-E7 immunity protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsChak, K.-F. / Safo, M.K. / Ku, W.-Y. / Hsieh, S.-Y. / Yuan, H.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: The crystal structure of the immunity protein of colicin E7 suggests a possible colicin-interacting surface.
Authors: Chak, K.F. / Safo, M.K. / Ku, W.Y. / Hsieh, S.Y. / Yuan, H.S.
History
DepositionMar 19, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: 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

Downloads & links

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Assembly

Deposited unit
A: COLICIN E7 IMMUNITY PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,6521
Polymers10,6521
Non-polymers00
Water1,08160
1
A: COLICIN E7 IMMUNITY PROTEIN

A: COLICIN E7 IMMUNITY PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,3042
Polymers21,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)75.140, 50.480, 45.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsTHERE IS ONE MONOMER IN THE ASYMMETRIC UNIT. THE FIRST TWO N-TERMINAL RESIDUES ARE DISORDERED AND ARE NOT OBSERVED IN THE ELECTRON DENSITY MAP.

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Components

#1: Protein COLICIN E7 IMMUNITY PROTEIN / IMME7


Mass: 10651.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q03708
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growpH: 8 / Details: pH 8.
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
21.2 Mammonium phosphate1drop
33.0 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 21, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 7917 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 3.97 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.9 / % possible all: 78.1
Reflection
*PLUS
Num. measured all: 31416
Reflection shell
*PLUS
% possible obs: 78.1 %

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Processing

Software
NameClassification
X-PLORrefinement
MSCdata reduction
MSCdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.187 --
obs0.187 7672 95.3 %
Displacement parametersBiso mean: 28.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms681 0 0 60 741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.132
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.09
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.07
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.09

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