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- PDB-3eip: CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO... -

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Basic information

Entry
Database: PDB / ID: 3eip
TitleCRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE
ComponentsPROTEIN (COLICIN E3 IMMUNITY PROTEIN)
KeywordsIMMUNE SYSTEM / RIBONUCLEASE INHIBITOR / COLICIN
Function / homology
Function and homology information


bacteriocin immunity / toxic substance binding
Similarity search - Function
Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Chitinase A; domain 3 / Roll / Alpha Beta
Similarity search - Domain/homology
Colicin E3 immunity protein
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.8 Å
AuthorsLi, C. / Zhao, D. / Djebli, A. / Shoham, M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase.
Authors: Li, C. / Zhao, D. / Djebli, A. / Shoham, M.
History
DepositionMar 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (COLICIN E3 IMMUNITY PROTEIN)
B: PROTEIN (COLICIN E3 IMMUNITY PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6253
Polymers19,5592
Non-polymers651
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-47 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.070, 53.720, 36.250
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98758, -0.05027, 0.14884), (-0.15473, 0.14727, -0.97692), (0.02719, -0.98782, -0.15322)
Vector: 34.51748, 49.62875, 54.27967)

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Components

#1: Protein PROTEIN (COLICIN E3 IMMUNITY PROTEIN)


Mass: 9779.565 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ZINC BOUND BETWEEN CYS 47 OF A AND B CHAINS
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110
Description: OVEREXPRESSION BY ADDTION OF MITOMYCIN C DURING LOG PHASE OF GROWTH
Plasmid: COLE3 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P02984
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.99 Å3/Da / Density % sol: 37 %
Crystal growpH: 6
Details: 2.0 M AMMONIUM SULFATE, 0.1 M MES BUFFER, PH 6.0, pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21.4 Mammonium sulfate1drop
380 mMsodium chloride1drop
433 mMMES1drop
50.005 mMsodium azide1drop
60.005 mMPMSF1drop
72 Mammonium sulfate1reservoir
8100 mMMES1reservoir
9100 mMsodium chloride1reservoir
1010 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Aug 1, 1993
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→44.6 Å / Num. obs: 11806 / % possible obs: 80 % / Redundancy: 2.03 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 41.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.56 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 2.5 / % possible all: 0.78
Reflection
*PLUS
Num. obs: 11860 / % possible obs: 81 %
Reflection shell
*PLUS
% possible obs: 77 % / Rmerge(I) obs: 0.167

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.4Arefinement
SDMSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 1.8→44.6 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 1175 10 %RANDOM
Rwork0.2178 ---
obs-11860 80 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 36.53 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 23.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-2.5 Å2
2--2.525 Å20 Å2
3----1.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 1 118 1505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.58
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→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.375 125 10 %
Rwork0.2798 959 -
obs--0.78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4A / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.265 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.58
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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