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Yorodumi- PDB-4bi8: Crystal structure of the type VI effector-immunity complex Ssp1-R... -
+Open data
-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 | ||||||
Components |
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Keywords | TOXIN / PROTEIN RAP1A COMPLEX | ||||||
Function / homology | Function and homology information 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 | SERRATIA MARCESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Srikannathasan, V. / Coulthurst, S.J. / Hunter, W.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bi8.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bi8.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/4bi8 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/4bi8 | HTTPS FTP |
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-Related structure data
Related structure data | 3zfiC 3zibC 4bi3SC 4bi4C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 Description: SEQUENCE DATA NOT AVAILABLE IN UNIPROT DATABASE Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S4S1W3*PLUS |
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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.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 Description: SEQUENCE DATA NOT AVAILABLE IN UNIPROT DATABASE Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S4S1W1*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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