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- PDB-1ujz: Crystal structure of the E7_C/Im7_C complex; a computationally de... -

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Basic information

Entry
Database: PDB / ID: 1ujz
TitleCrystal structure of the E7_C/Im7_C complex; a computationally designed interface between the colicin E7 DNase and the Im7 Immunity protein
Components
  • Designed Colicin E7 DNase
  • Designed Colicin E7 immunity protein
KeywordsIMMUNE SYSTEM / computational design / redesigned protein-protein interface / specificity / molecular recognition / protein complex
Function / homology
Function and homology information


extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / metal ion binding
Similarity search - Function
Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / 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 / HNH nucleases / His-Me finger superfamily / HNH nuclease / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Colicin-E7 immunity protein / Colicin-E7
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKortemme, T. / Joachimiak, L.A. / Bullock, A.N. / Schuler, A.D. / Stoddard, B.L. / Baker, D.
CitationJournal: NAT.STRUCT.MOL.BIOL. / Year: 2004
Title: Computational redesign of protein-protein interaction specificity
Authors: Kortemme, T. / Joachimiak, L.A. / Bullock, A.N. / Schuler, A.D. / Stoddard, B.L. / Baker, D.
History
DepositionAug 13, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 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

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Assembly

Deposited unit
A: Designed Colicin E7 immunity protein
B: Designed Colicin E7 DNase


Theoretical massNumber of molelcules
Total (without water)24,6622
Polymers24,6622
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.882, 74.552, 120.444
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 Designed Colicin E7 immunity protein / dC immunity protein / Im7


Mass: 9955.049 Da / Num. of mol.: 1 / Mutation: D35Y,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CEIE7 / Plasmid: PHBH / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q03708
#2: Protein Designed Colicin E7 DNase / dC DNase


Mass: 14706.647 Da / Num. of mol.: 1 / Fragment: residues 446-573 / Mutation: K528Q, T539R, H569A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CEIE7 / Plasmid: PHBH / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009
References: UniProt: Q47112, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.77 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEGMME 2000, ammonium sulfate, Sodium Acetate, Glycerol, DMSO, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 11, 2002
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 33148 / Num. obs: 19513 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.1 Å2 / Net I/σ(I): 39.8
Reflection shellResolution: 2.07→2.15 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7cei

7cei


Resolution: 2.1→37.57 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 274027.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1615 9.8 %RANDOM
Rwork0.242 ---
all0.262 ---
obs0.242 16460 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.576 Å2 / ksol: 0.38722 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å20 Å2
2--4.6 Å20 Å2
3----7.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 0 91 1819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 268 10.3 %
Rwork0.245 2328 -
obs-2734 93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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