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

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Basic information

Entry
Database: PDB / ID: 3gjn
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 / Bacteriocin immunity / Antibiotic / Antimicrobial / Bacteriocin / Endonuclease / Metal-binding / Nuclease
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, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / 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, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsDym, O. / Tawfik, D.S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Following evolutionary paths to protein-protein interactions with high affinity and selectivity
Authors: Levin, K.B. / Dym, O. / Albeck, S. / Magdassi, S. / Keeble, A.H. / Kleanthous, C. / Tawfik, D.S.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Experimental preparation
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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-E7
C: Colicin-E7
D: Colicin-E9 immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8816
Polymers51,7504
Non-polymers1312
Water27015
1
A: Colicin-E9 immunity protein


Theoretical massNumber of molelcules
Total (without water)9,6451
Polymers9,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Colicin-E7
D: Colicin-E9 immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9403
Polymers25,8752
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Colicin-E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2962
Polymers16,2301
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Colicin-E9 immunity protein


Theoretical massNumber of molelcules
Total (without water)9,6451
Polymers9,6451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.650, 53.713, 79.334
Angle α, β, γ (deg.)90.00, 105.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 6

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA1004 - 10854 - 85
21GLNGLNDD1004 - 10854 - 85
12LYSLYSBB452 - 57617 - 141
22LYSLYSCC452 - 57617 - 141

NCS ensembles :
ID
1
2

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Components

#1: Protein Colicin-E9 immunity protein / ImmE9 / Microcin-E9 immunity protein


Mass: 9644.530 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
#2: Protein Colicin-E7


Mass: 16230.438 Da / Num. of mol.: 2 / Fragment: UNP residues 446-576
Mutation: N1024D, D1026E, T1027A, S1028T, V1034D, V1037I, Y1055W
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
#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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 292 K / pH: 10.5
Details: 30% PEG40, pH10.5, Microbatch under oil, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2007 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 15983 / % possible obs: 94.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.86 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.143 / Net I/σ(I): 8.63
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1405 / Rsym value: 0.276 / % possible all: 83.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FR2, 1ZNV

1fr2

1znv


Resolution: 2.48→43.94 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.279 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.766 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27566 814 5.1 %RANDOM
Rwork0.24233 ---
obs0.24403 15160 91.86 %-
all-16503 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.864 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-3.75 Å2
2---4.03 Å20 Å2
3---3.47 Å2
Refinement stepCycle: LAST / Resolution: 2.48→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 2 15 3243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223292
X-RAY DIFFRACTIONr_angle_refined_deg2.5111.9474422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2715397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56524.878164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.06115612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2481520
X-RAY DIFFRACTIONr_chiral_restr0.1770.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022498
X-RAY DIFFRACTIONr_nbd_refined0.2820.21493
X-RAY DIFFRACTIONr_nbtor_refined0.3250.22204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2130
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.22
X-RAY DIFFRACTIONr_mcbond_it1.511.52085
X-RAY DIFFRACTIONr_mcangle_it2.08923233
X-RAY DIFFRACTIONr_scbond_it3.54831406
X-RAY DIFFRACTIONr_scangle_it5.2364.51189
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A647loose positional0.245
2B955loose positional0.155
1A647loose thermal1.1710
2B955loose thermal1.3710
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 45 -
Rwork0.299 619 -
obs--52.37 %

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