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- PDB-1emv: CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1emv | ||||||
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Title | CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS) | ||||||
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![]() | IMMUNE SYSTEM / protein-protein complex | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kuhlmann, U.C. / Pommer, A.J. / Moore, G.M. / James, R. / Kleanthous, C. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.2 KB | Display | ![]() |
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PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
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Full document | ![]() | 445.4 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a heterodimeric complex of the E9 DNase domain with its cognate immunity protein Im9 |
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Components
#1: Protein | Mass: 9592.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | 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.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Compound details | E9 DNase is metal free |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.89 % | |||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Resolution: 1.7→20 Å / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 39.5367 Å2 / ksol: 0.342601 e/Å3 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Xplor file |
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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 |