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- PDB-4bi3: Structure and function of amidase toxin - antitoxin combinations ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bi3 | ||||||
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Title | Structure and function of amidase toxin - antitoxin combinations associated with the type VI secretion system of Serratia marcescens. | ||||||
![]() | SSP1 | ||||||
![]() | TOXIN | ||||||
Function / homology | ![]() endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Srikannathasan, V. / English, G. / Bui, N.K. / Trunk, K. / Rourke, P.E.F.O. / Rao, V.A. / Vollmer, W. / Coulthurst, S.J. / Hunter, W.N. | ||||||
![]() | ![]() Title: Structural Basis for Type Vi Secreted Peptidoglycan Dl-Endopeptidase Function, Specificity and Neutralization in Serratia Marcescens Authors: Srikannathasan, V. / English, G. / Bui, N.K. / Trunk, K. / Rourke, P.E.F.O. / Rao, V.A. / Vollmer, W. / Coulthurst, S.J. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
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Full document | ![]() | 443 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18205.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 6.4 / Details: 0.2M POTASSIUM SULPHATE, 20% PEG3350, pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU (SATURN 944 HG) / Detector: CCD / Date: Jun 29, 2012 |
Radiation | Monochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.75 Å / Num. obs: 31054 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 16 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 10.2 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.85→54.23 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.061 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.425 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→54.23 Å
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Refine LS restraints |
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