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- PDB-2gyk: Crystal structure of the complex of the Colicin E9 DNase domain w... -

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Basic information

Entry
Database: PDB / ID: 2gyk
TitleCrystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)
Components
  • Colicin-E9
  • Colicin-E9 immunity protein
Keywordsantibiotic/antibiotic inhibitor / PROTEIN-PROTEIN COMPLEX / 4-HELIX BUNDLE / DNASE DOMAIN / HNH-MOTIF / antibiotic-antibiotic inhibitor 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 / 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 / His-Me finger superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Colicin-E9 / Colicin-E9 immunity protein
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSanti, P.S. / Kolade, O.O. / Kuhlmann, U.C. / Hemmings, A.M.
Citation
Journal: To be Published
Title: Crystal structures of the complexes of the Colicin E9 DNase domain with mutant immunity proteins
Authors: Kuhlmann, U.C. / Santi, P.S. / Kolade, O.O. / Moore, G.R. / James, R. / Kleanthous, C. / Hemmings, A.M.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: Structural and mechanistic basis of immunity towards endonuclease colicins
Authors: Kleanthous, C. / Kuhlmann, U.C. / Pommer, A.J. / Ferguson, N. / Radford, S.E. / Moore, G.R. / James, R. / Hemmings, A.M.
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Refinement description / Category: diffrn / 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 / pdbx_struct_conn_angle ...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_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_conn.ptnr2_label_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
Revision 1.5Aug 30, 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
E: Colicin-E9 immunity protein
F: Colicin-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6588
Polymers49,3374
Non-polymers3214
Water12,358686
1
A: Colicin-E9 immunity protein
B: Colicin-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8294
Polymers24,6692
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-53 kcal/mol
Surface area11150 Å2
MethodPISA
2
E: Colicin-E9 immunity protein
F: Colicin-E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8294
Polymers24,6692
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-54 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.903, 88.248, 52.235
Angle α, β, γ (deg.)90.000, 91.920, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A DIMER OF THE BIOLOGICAL UNIT

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Components

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


Mass: 9548.490 Da / Num. of mol.: 2 / Mutation: D51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: IMM9_ECOLI / Plasmid: pET21D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13479
#2: Protein Colicin-E9


Mass: 15120.021 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, DNASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: col, cei / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P09883, deoxyribonuclease I
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Temp details: 277

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000
RadiationMonochromator: SILICON(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 51260 / Num. obs: 51260 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.027 / Χ2: 1.422 / Net I/σ(I): 34.4
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.045 / Num. unique all: 4468 / Χ2: 0.593 / % possible all: 84.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0003refinement
PDB_EXTRACT2data extraction
ADSCdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMV

1emv


Resolution: 1.6→19.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.39 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2598 5.1 %RANDOM
Rwork0.185 ---
all0.187 53245 --
obs0.187 51228 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 12 686 4071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223499
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9484721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30624.878164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35315646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6861519
X-RAY DIFFRACTIONr_chiral_restr0.090.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022653
X-RAY DIFFRACTIONr_nbd_refined0.20.21678
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2463
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.271
X-RAY DIFFRACTIONr_mcbond_it0.8051.52220
X-RAY DIFFRACTIONr_mcangle_it1.24823484
X-RAY DIFFRACTIONr_scbond_it2.14931452
X-RAY DIFFRACTIONr_scangle_it3.3094.51235
LS refinement shellResolution: 1.6→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 160 -
Rwork0.199 2893 -
obs-3053 79.03 %

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