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- PDB-2yn5: Structural insight into the giant calcium-binding adhesin SiiE: i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yn5 | ||||||
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Title | Structural insight into the giant calcium-binding adhesin SiiE: implications for the adhesion of Salmonella enterica to polarized epithelial cells | ||||||
![]() | PUTATIVE INNER MEMBRANE PROTEIN | ||||||
![]() | MEMBRANE PROTEIN / BIG-DOMAINS ADHESIN | ||||||
Function / homology | ![]() homophilic cell adhesion via plasma membrane adhesion molecules / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Griessl, M.H. / Schmid, B. / Kassler, K. / Braunsmann, C. / Ritter, R. / Barlag, B. / Sturm, K.U. / Danzer, C. / Wagner, C. / Schaeffer, T.E. ...Griessl, M.H. / Schmid, B. / Kassler, K. / Braunsmann, C. / Ritter, R. / Barlag, B. / Sturm, K.U. / Danzer, C. / Wagner, C. / Schaeffer, T.E. / Sticht, H. / Hensel, M. / Muller, Y.A. | ||||||
![]() | ![]() Title: Structural Insight Into the Giant Ca(2+)-Binding Adhesin Siie: Implications for the Adhesion of Salmonella Enterica to Polarized Epithelial Cells. Authors: Griessl, M.H. / Schmid, B. / Kassler, K. / Braunsmann, C. / Ritter, R. / Barlag, B. / Stierhof, Y. / Sturm, K.U. / Danzer, C. / Wagner, C. / Schaffer, T.E. / Sticht, H. / Hensel, M. / Muller, Y.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Crystallization and Preliminary Crystallographic Analysis of an Ig-Domain-Encompassing Fragment of the Giant Adhesion Protein Siie from Salmonella Enterica. Authors: Sturm, K.U. / Griessl, M.H. / Wagner, C. / Deiwick, J. / Hensel, M. / Muller, Y.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.1 KB | Display | ![]() |
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PDB format | ![]() | 96.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.9 KB | Display | ![]() |
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Full document | ![]() | 429.5 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yn3SC 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
#1: Protein | Mass: 30281.018 Da / Num. of mol.: 2 / Fragment: BIG DOMAINS 50 TO 52, RESIDUES 5078-5365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / Plasmid: P3355-1 / Production host: ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 6.7 Details: 0.1 M SODIUM CACODYLATE, PH 6.7, 0.2 M CALCIUM ACETATE, 16 % W/V PEG 8000, 3% 6-AMINOHEXANOIC ACID |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 50496 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YN3 Resolution: 1.85→47 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.533 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 21.511 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→47 Å
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Refine LS restraints |
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