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- PDB-1unk: STRUCTURE OF COLICIN E7 IMMUNITY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1unk
TitleSTRUCTURE OF COLICIN E7 IMMUNITY PROTEIN
ComponentsCOLICIN E7
KeywordsIMMUNITY PROTEIN / DIMERIC STRUCTURE / RNASE ACTIVE SITE
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 / Resolution: 1.8 Å
AuthorsKo, T.-P. / Hsieh, S.-Y. / Ku, W.-Y. / Tseng, M.-Y. / Chak, K.-F. / Yuan, H.S.
CitationJournal: EMBO J. / Year: 1997
Title: A novel role of ImmE7 in the autoregulatory expression of the ColE7 operon and identification of possible RNase active sites in the crystal structure of dimeric ImmE7.
Authors: Hsieh, S.Y. / Ko, T.P. / Tseng, M.Y. / Ku, W. / Chak, K.F. / Yuan, H.S.
History
DepositionJun 21, 1996Processing site: BNL
Revision 1.0Jan 7, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
B: COLICIN E7
C: COLICIN E7
D: COLICIN E7


Theoretical massNumber of molelcules
Total (without water)39,6284
Polymers39,6284
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.900, 101.700, 52.600
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHERE ARE 4 MOLECULES PER ASYMMETRIC UNIT, EACH HAVING 87 RESIDUES.

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Components

#1: Protein
COLICIN E7 / IMMUNITY E7 PROTEIN / IMME7


Mass: 9906.963 Da / Num. of mol.: 4 / 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.: 127 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMONOMERIC FORM BINDS SPECIFICALLY TO COLE7 AS AN INHIBITOR. DIMERIC FORM MAY HAVE NOVEL RNASE ACTIVITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 40 %
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

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 4, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 28088 / % possible obs: 97.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Num. measured all: 182726

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MSCdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→6 Å / Cross valid method: BRUNGER / σ(F): 2
Details: SET OF IDEAL BOND LENGTHS AND ANGLES USED DURING REFINEMENT MODIFIED CHARMM FILES
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1977 8 %RANDOM
Rwork0.18 ---
obs0.18 24738 90.4 %-
Displacement parametersBiso mean: 27.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 0 127 2919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg1.935
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
LS refinement shellResolution: 1.8→1.83 Å
RfactorNum. reflection% reflection
Rfree0.333 75 8.4 %
Rwork0.301 821 -
obs--66.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 24783 / Rfactor Rfree: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.301

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