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- PDB-1ayi: COLICIN E7 IMMUNITY PROTEIN IM7 -

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Basic information

Entry
Database: PDB / ID: 1ayi
TitleCOLICIN E7 IMMUNITY PROTEIN IM7
ComponentsCOLICIN E IMMUNITY PROTEIN 7
KeywordsBACTERIOCIN / E COLICINS / PROTEIN-PROTEIN INTERACTIONS / DNASE INHIBITOR
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDennis, C.A. / Pauptit, R.A. / Wallis, R. / James, R. / Moore, G.R. / Kleanthous, C.
CitationJournal: Biochem.J. / Year: 1998
Title: A structural comparison of the colicin immunity proteins Im7 and Im9 gives new insights into the molecular determinants of immunity-protein specificity.
Authors: Dennis, C.A. / Videler, H. / Pauptit, R.A. / Wallis, R. / James, R. / Moore, G.R. / Kleanthous, C.
History
DepositionNov 4, 1997Processing site: BNL
Revision 1.0Jan 28, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLICIN E IMMUNITY PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)9,9071
Polymers9,9071
Non-polymers00
Water61334
1
A: COLICIN E IMMUNITY PROTEIN 7

A: COLICIN E IMMUNITY PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)19,8142
Polymers19,8142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)44.630, 50.677, 75.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein COLICIN E IMMUNITY PROTEIN 7 / IM7


Mass: 9906.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q03708
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.14 Å3/Da / Density % sol: 41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.2
Details: USING THE HANGING DROP METHOD, PROTEIN (10MG/ML) WAS CRYSTALLISED BY MIXING AN EQUAL VOLUME OF PROTEIN WITH A SOLUTION CONTAINING 55% SATURATED DI-AMMONIUM PHOSPHATE AND 200MM TRIS PH7.2. ...Details: USING THE HANGING DROP METHOD, PROTEIN (10MG/ML) WAS CRYSTALLISED BY MIXING AN EQUAL VOLUME OF PROTEIN WITH A SOLUTION CONTAINING 55% SATURATED DI-AMMONIUM PHOSPHATE AND 200MM TRIS PH7.2. THE DROP WAS EQUILIBRATED AGAINST A WELL CONTAINING 100% SATURATED DI-AMMONIUM PHOSPHATE AT ROOM TEMPERATURE., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
255 %satdi-ammonium phosphate1drop
3200 mMTris-HCl1drop
4100 %satdi-ammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 5828 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.049 / Net I/σ(I): 14
Reflection shellResolution: 2→2.18 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.156 / % possible all: 87
Reflection
*PLUS
Num. measured all: 19772 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.156

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
XDSdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 10 ALIGNED NMR STRUCTURES OF COLICIN E9 IMMUNITY PROTEIN IM9

Resolution: 2→10 Å / Cross valid method: THROUGHOUT
Details: X-PLOR WAS USED INITIALLY TO REFINE THE VERY INCOMPLETE STARTING MODEL FROM MOLECULAR REPLACEMENT. THE REFINEMENT USING SIMULATED ANNEALING AND POSITIONAL REFINEMENT DID NOT DECREASE THE ...Details: X-PLOR WAS USED INITIALLY TO REFINE THE VERY INCOMPLETE STARTING MODEL FROM MOLECULAR REPLACEMENT. THE REFINEMENT USING SIMULATED ANNEALING AND POSITIONAL REFINEMENT DID NOT DECREASE THE FREE R VALUE. AT THIS STAGE, REFINEMENT BY MAXIMUM LIKELIHOOD METHOD WAS STARTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 500 10 %RANDOM
Rwork0.178 ---
obs-5000 --
Displacement parametersBiso mean: 21.6 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 0 44 714
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.5
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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