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- PDB-1emv: CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMM... -

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Basic information

Entry
Database: PDB / ID: 1emv
TitleCRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS)
Components
  • COLICIN E9
  • IMMUNITY PROTEIN IM9
KeywordsIMMUNE SYSTEM / protein-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 / 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKuhlmann, U.C. / Pommer, A.J. / Moore, G.M. / James, R. / Kleanthous, C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes.
Authors: Kuhlmann, U.C. / Pommer, A.J. / Moore, G.R. / James, R. / Kleanthous, C.
History
DepositionMar 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNITY PROTEIN IM9
B: COLICIN E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8073
Polymers24,7132
Non-polymers951
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-12 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.870, 52.560, 87.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterodimeric complex of the E9 DNase domain with its cognate immunity protein Im9

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Components

#1: Protein IMMUNITY PROTEIN IM9 / IMME9 / MICROCIN E9 IMMUNITY PROTEIN


Mass: 9592.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTRC 99A (PRJ352) / Production host: Escherichia coli (E. coli) / References: UniProt: P13479
#2: Protein COLICIN E9


Mass: 15120.021 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, DNASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTRC 99A (PRJ352) / Production host: Escherichia coli (E. coli) / References: UniProt: P09883, deoxyribonuclease I
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Compound detailsE9 DNase is metal free

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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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 24% PEG 4000, 0.1M sodium acetate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Details: used seeding, Kuhlmann, U.C., (1999) Acta. Crystallog. sect. D55, 256.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
132 %(w/v)PEG40001reservoir
20.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 20868 / Num. obs: 20871 / % possible obs: 89.9 % / Observed criterion σ(F): 1.14 / Observed criterion σ(I): 3.85 / Redundancy: 19.8 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 47.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Num. unique all: 330 / % possible all: 73.4
Reflection
*PLUS
Num. measured all: 415140
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 73.4 % / Mean I/σ(I) obs: 16.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.7→20 Å / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1098 -RANDOM
Rwork0.219 ---
all-22962 --
obs-20724 90.3 %-
Solvent computationBsol: 39.5367 Å2 / ksol: 0.342601 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 5 154 1849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.538
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4dna-rna_rep.param
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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