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- PDB-4bi8: Crystal structure of the type VI effector-immunity complex Ssp1-R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bi8 | ||||||
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Title | Crystal structure of the type VI effector-immunity complex Ssp1-Rap1a from Serratia marcescens | ||||||
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![]() | TOXIN / PROTEIN RAP1A COMPLEX | ||||||
Function / homology | ![]() 10k-s Protein, Hypothetical Protein A; Chain A - #40 / endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / 10k-s Protein, Hypothetical Protein A; Chain A / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) ...10k-s Protein, Hypothetical Protein A; Chain A - #40 / endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / 10k-s Protein, Hypothetical Protein A; Chain A / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Srikannathasan, V. / 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 | ![]() | 116.3 KB | Display | ![]() |
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PDB format | ![]() | 90.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.1 KB | Display | ![]() |
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Full document | ![]() | 430 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zfiC ![]() 3zibC ![]() 4bi3SC ![]() 4bi4C S: Starting model for refinement C: citing same article ( |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11500.976 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: SEQUENCE DATA NOT AVAILABLE IN UNIPROT DATABASE Production host: ![]() ![]() |
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#2: Protein | Mass: 18205.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: SEQUENCE DATA NOT AVAILABLE IN UNIPROT DATABASE Production host: ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Details: 12.5% PEG1K, 12.5% PEG3350 AND 12.5% MPD. 20% GLYCEROL AS A CRYO-PROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 HG / Detector: CCD / Date: Oct 23, 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: 2→49.92 Å / Num. obs: 17462 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 28.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 40.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 25.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 11.4 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BI3 Resolution: 2→49.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.711 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.166 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.653 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.92 Å
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Refine LS restraints |
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