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Open data
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Basic information
Entry | Database: PDB / ID: 3zfi | ||||||
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Title | Rap1a protein (SMA2260) from Serratia marcescens | ||||||
![]() | RAP1A PROTEIN | ||||||
![]() | TRANSPORT PROTEIN / BACTERIAL IMMUNITY / 2260 PROTEIN / T6SS / TYPE VI SECRETION SYSTEM / SELF-RESISTANCE PROTEIN | ||||||
Function / homology | 10k-s Protein, Hypothetical Protein A; Chain A - #40 / Rap1a immunity protein / Rap1a immunity proteins / 10k-s Protein, Hypothetical Protein A; Chain A / Orthogonal Bundle / Mainly Alpha / Rap1a protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Srikannathasan, V. / O'Rourke, P.E.F. / Rao, V.A. / English, G. / 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 | ![]() | 46.6 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.3 KB | Display | ![]() |
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Full document | ![]() | 432 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.6 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: 11827.369 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN (SIGNAL PEPTIDE CLEAVED) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: SITTING DROP VAPOUR DIFFUSION. PROTEIN CONCENTRATION AT 9MG/ML, IN 150 MM SODIUM CHLORIDE, 25MM TRIS-HCL, PH 7.5 (SAMPLE BUFFER) RESERVOIR: 25% W/V POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS, ...Details: SITTING DROP VAPOUR DIFFUSION. PROTEIN CONCENTRATION AT 9MG/ML, IN 150 MM SODIUM CHLORIDE, 25MM TRIS-HCL, PH 7.5 (SAMPLE BUFFER) RESERVOIR: 25% W/V POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS, PH 5.5 2:1 SAMPLE TO RESERVOIR RATIO. |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2011 / Details: COMPOUND REFRACTIVE LENSES |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→46.5 Å / Num. obs: 14089 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 37.714 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→61.78 Å
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Refine LS restraints |
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