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- PDB-3u43: Crystal structure of the colicin E2 DNase-Im2 complex -

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Basic information

Entry
Database: PDB / ID: 3u43
TitleCrystal structure of the colicin E2 DNase-Im2 complex
Components
  • Colicin-E2
  • Colicin-E2 immunity protein
KeywordsPROTEIN BINDING / protein-protein complex / DNase / high affinity
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, 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-E2 / Colicin-E2 immunity protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsWojdyla, J.A. / Kleanthous, C.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structure of the Ultra-High-Affinity Colicin E2 DNase-Im2 Complex.
Authors: Wojdyla, J.A. / Fleishman, S.J. / Baker, D. / Kleanthous, C.
History
DepositionOct 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Colicin-E2 immunity protein
B: Colicin-E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5554
Polymers26,4502
Non-polymers1052
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-44 kcal/mol
Surface area12310 Å2
MethodPISA
2
B: Colicin-E2
hetero molecules

A: Colicin-E2 immunity protein


Theoretical massNumber of molelcules
Total (without water)26,5554
Polymers26,4502
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1310 Å2
ΔGint-54 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.814, 53.277, 32.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Colicin-E2 immunity protein / ImmE2 / Microcin-E2 immunity protein


Mass: 11082.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: imm, ceiB / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P04482
#2: Protein Colicin-E2


Mass: 15367.430 Da / Num. of mol.: 1 / Fragment: DNase domain (UNP residues 449-581)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: col, ceaB / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: P04419, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MMT, 27% PEG1500, pH 7.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.714→121.814 Å / Num. obs: 23549 / % possible obs: 99.1 % / Redundancy: 6.9 % / Rsym value: 0.084 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.71-1.815.20.4271.81659831740.42793.9
1.81-1.927.30.2872.72343432260.287100
1.92-2.057.30.1844.22221330570.184100
2.05-2.217.30.135.82060928320.13100
2.21-2.427.30.1017.31903326250.101100
2.42-2.717.20.0828.81726723830.082100
2.71-3.137.20.0719.61522221190.071100
3.13-3.837.10.05911.11294518200.059100
3.83-5.426.90.04912.61001114450.049100
5.42-48.8136.30.0415.554768680.0499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å48.81 Å
Translation1.95 Å48.81 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→48.81 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.1939 / WRfactor Rwork: 0.1526 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8812 / SU B: 2.145 / SU ML: 0.071 / SU R Cruickshank DPI: 0.115 / SU Rfree: 0.1118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1206 5.1 %RANDOM
Rwork0.1616 ---
all0.1638 23419 --
obs0.1638 23419 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.62 Å2 / Biso mean: 18.213 Å2 / Biso min: 5.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.77 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 2 319 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211937
X-RAY DIFFRACTIONr_angle_refined_deg2.141.9472601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29223.774106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83715379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6041518
X-RAY DIFFRACTIONr_chiral_restr0.1590.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211509
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 70 -
Rwork0.279 1409 -
all-1479 -
obs--95.98 %

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