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- PDB-1jch: Crystal Structure of Colicin E3 in Complex with its Immunity Protein -

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Basic information

Entry
Database: PDB / ID: 1jch
TitleCrystal Structure of Colicin E3 in Complex with its Immunity Protein
Components
  • COLICIN E3
  • COLICIN E3 IMMUNITY PROTEIN
KeywordsRIBOSOME INHIBITOR / HYDROLASE / TRANSLOCATION DOMAIN IS A BETA-JELLYROLL / THE RECEPTOR-BINDING DOMAIN IS A COILED COIL / THE RNASE DOMAIN IS A SIX-STRANDED ANTIPARALLEL BETA-SHEET. THE IMMUNITY PROTEIN IS A FOUR-STRANDED ANTIPARALLEL BETA SHEET FLANKED BY 3 HELICES ON ONE SIDE OF THE SHEET
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / tRNA binding ...negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / tRNA binding / rRNA binding / defense response to bacterium / lyase activity / extracellular region
Similarity search - Function
Helix Hairpins / Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic ...Helix Hairpins / Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / S-type Pyocin / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Chitinase A; domain 3 / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Colicin E3 / Colicin E3 immunity protein
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.02 Å
AuthorsSoelaiman, S. / Jakes, K. / Wu, N. / Li, C. / Shoham, M.
CitationJournal: Mol.Cell / Year: 2001
Title: Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
Authors: Soelaiman, S. / Jakes, K. / Wu, N. / Li, C. / Shoham, M.
History
DepositionJun 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 BIOLOGICAL UNITS. THE FIRST BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A+B AND HETGROUPS CIT 601 AND 602, GOL 701 AND 702 AND HOH RESIDUES NOT STARTING WITH A PREFIX 5000. THE SECOND BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS C+D AND HETGROUPS CIT 5601 AND 5602, GOL 5701 AND 5702 AND HOH RESIDUES STARTING WITH A PREFIX 5000.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLICIN E3
B: COLICIN E3 IMMUNITY PROTEIN
C: COLICIN E3
D: COLICIN E3 IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,78212
Polymers135,6454
Non-polymers1,1378
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: COLICIN E3
B: COLICIN E3 IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3916
Polymers67,8232
Non-polymers5684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-25 kcal/mol
Surface area29470 Å2
MethodPISA
3
C: COLICIN E3
D: COLICIN E3 IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3916
Polymers67,8232
Non-polymers5684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-25 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.986, 195.733, 85.124
Angle α, β, γ (deg.)90.00, 113.22, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99997, 0.00024, 0.00756), (-0.00024, -1, -0.00042), (0.00756, -0.00042, 0.99997)33.34507, 148.82249, -0.00929
DetailsCOLICIN E3 FORMS A DIMER IN SOLUTION AS WELL AS IN THE CRYSTALLINE STATE. THE SECOND MOLECULE IN THE ASYMMETRIC UNIT CAN BE GENERATED BY THE FOLLOWING MATRIX: -0.99997 0.00024 0.00756, -0.00024 -1.00000 -0.00042, 0.00756 -0.00042 0.99997, AND TRANSLATION VECTOR IN ANGSTROMS: 33.345 148.822 -0.009

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Components

#1: Protein COLICIN E3 / E.C.3.1.21.- / RIBONUCLEASE / COLICIN E3 A CHAIN


Mass: 58043.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110
References: UniProt: P00646, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Protein COLICIN E3 IMMUNITY PROTEIN / IMME3 / MICROCIN E3 IMMUNITY PROTEIN / COLICIN E3 CHAIN B / immunity protein 2


Mass: 9779.565 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P02984
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
Conc.: 1 M / Common name: sodium citrate / Details: pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.037 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 3.02→20 Å / Num. all: 37014 / Num. obs: 37014 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3509 / % possible all: 86.4

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.02→20.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2270567.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1127 3 %RANDOM
Rwork0.237 ---
all0.237 37014 --
obs0.237 37014 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.5511 Å2 / ksol: 0.26419 e/Å3
Displacement parametersBiso mean: 74.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.48 Å20 Å28.68 Å2
2---8.29 Å20 Å2
3---1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-10 Å
Luzzati sigma a0.56 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.02→20.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 76 396 8998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_mcbond_it11.061.5
X-RAY DIFFRACTIONc_mcangle_it15.832
X-RAY DIFFRACTIONc_scbond_it16.322
X-RAY DIFFRACTIONc_scangle_it20.872.5
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 80 2.6 %
Rwork0.323 2973 -
obs-2973 60.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIT.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMCIT.TOP
X-RAY DIFFRACTION5GLYCEROL.PARAMGLYCEROL.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.233 / Rfactor Rfree: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 74.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41
X-RAY DIFFRACTIONc_mcbond_it11.061.5
X-RAY DIFFRACTIONc_scbond_it16.322
X-RAY DIFFRACTIONc_mcangle_it15.832
X-RAY DIFFRACTIONc_scangle_it20.872.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / % reflection Rfree: 2.6 % / Rfactor Rwork: 0.323

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