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- PDB-2b5u: Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its ... -

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Basic information

Entry
Database: PDB / ID: 2b5u
TitleCrystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein
Components
  • Colicin E3
  • Colicin E3 immunity protein
KeywordsRIBOSOME INHIBITOR / HYDROLASE / High resolution crystal structure / Colicin E3 / Immunity Protein / Ribosome inactivation
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / Hydrolases; Acting on ester bonds / defense response to bacterium / RNA binding
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsNallini Vijayarangan, A. / Nithianantham, S. / Nan, W. / Jakes, K. / Shoham, M.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure Of Colicin E3 In Complex With Its Immunity Protein
Authors: Nallini Vijayarangan, A. / Nithianantham, S. / Nan, W. / Jakes, K. / Shoham, M.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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 E3
B: Colicin E3 immunity protein
C: Colicin E3
D: Colicin E3 immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0376
Polymers135,6534
Non-polymers3842
Water3,945219
1
A: Colicin E3
B: Colicin E3 immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0193
Polymers67,8272
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-22 kcal/mol
Surface area28830 Å2
MethodPISA
2
C: Colicin E3
D: Colicin E3 immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0193
Polymers67,8272
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-21 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.730, 192.916, 85.385
Angle α, β, γ (deg.)90.00, 112.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Colicin E3 / Colicin E3 A chain / Ribonuclease


Mass: 58047.023 Da / Num. of mol.: 2 / Mutation: V206C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ceaC / Plasmid: ColE3-CA38 / 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
#2: Protein Colicin E3 immunity protein / ImmE3 / Microcin E3 immunity protein / Colicin E3 chain B


Mass: 9779.565 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: imm, ceiC, immB / Plasmid: ColE3-CA38 / 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 / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 3.92 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.6
Details: Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorDetector: CCD / Date: Aug 3, 2005 / Details: Mirrors
RadiationMonochromator: Si-111, Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 88792 / Num. obs: 88240 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Χ2: 1
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 97.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.465 / Num. measured obs: 8682 / Χ2: 1.37 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JCH

1jch


Resolution: 2.3→44.4 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 8752 10 %RANDOM
Rwork0.259 ---
all0.295 88792 --
obs0.291 87291 99.4 %-
Solvent computationBsol: 39.605 Å2
Displacement parametersBiso mean: 51.725 Å2
Baniso -1Baniso -2Baniso -3
1--10.512 Å20 Å2-3.364 Å2
2--8.528 Å20 Å2
3---1.985 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8546 0 26 219 8791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007146
X-RAY DIFFRACTIONc_angle_deg1.29061
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3cit.param

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