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- PDB-3gkl: Following evolutionary paths to high affinity and selectivity pro... -

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Basic information

Entry
Database: PDB / ID: 3gkl
TitleFollowing evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins
Components
  • Colicin-E7
  • Colicin-E9 immunity protein
KeywordsHYDROLASE / Protein-Protein complex / Structural Genomics / Israel Structural Proteomics Center / ISPC / Bacteriocin immunity / Plasmid / Antibiotic / Antimicrobial / Bacteriocin / Endonuclease / Metal-binding / Nuclease / Zinc
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 / protein domain specific binding / protein-containing complex / 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-E9 immunity protein / Colicin-E7
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDym, O. / Tawfik, D.S. / Israel Structural Proteomics Center (ISPC)
CitationJournal: To be Published
Title: Following evolutionary paths to high affinity and selectivity protein-protein interactions
Authors: Bernath, K. / Dym, O. / Albeck, S. / Magdassi, S. / Keeble, A. / Kleanthous, C. / Tawfik, D.S.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Sep 6, 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-E9 immunity protein
B: Colicin-E9 immunity protein
C: Colicin-E7
D: Colicin-E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6026
Polymers51,4724
Non-polymers1312
Water18010
1
A: Colicin-E9 immunity protein
C: Colicin-E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8013
Polymers25,7362
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Colicin-E9 immunity protein
D: Colicin-E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8013
Polymers25,7362
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.161, 67.371, 123.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Colicin-E9 immunity protein


Mass: 16230.438 Da / Num. of mol.: 2 / Fragment: UNP residues 446-576 / Mutation: T20A, N24D, T27A, S28T, V34D, V37I, E41G, K57E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: colE7, cea / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q47112, Hydrolases; Acting on ester bonds
#2: Protein Colicin-E7 / ImmE9 / Microcin-E9 immunity protein


Mass: 9505.315 Da / Num. of mol.: 2 / Mutation: H545A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: imm, ceiE9 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13479
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 30% PEG 400, 0.1 CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 7, 2006
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: horizontally diffracting / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23137 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.12 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2 / Rsym value: 0.334 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GJN

3gjn


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.766 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27683 1147 5.1 %RANDOM
Rwork0.23956 ---
obs0.24139 21366 95.41 %-
all-21370 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.751 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å20 Å20 Å2
2--5.2 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 2 10 3225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0480.0223311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.8561.9494448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.275402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.16124.848165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.44115612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9781520
X-RAY DIFFRACTIONr_chiral_restr0.2740.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0212516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.350.21547
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.360.22122
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3510.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9141.52020
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.19823252
X-RAY DIFFRACTIONr_scbond_it4.99431291
X-RAY DIFFRACTIONr_scangle_it7.2454.51195
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 68 -
Rwork0.361 1567 -
obs--95.45 %

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