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Yorodumi- PDB-8alu: Crystal structure of the teichoic acid binding domain of SlpA, S-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8alu | ||||||
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Title | Crystal structure of the teichoic acid binding domain of SlpA, S-layer protein from Lactobacillus acidophilus (aa. 314-444) | ||||||
Components | S-layer protein | ||||||
Keywords | CELL ADHESION / s-layer / surface layer / cell wall binding / teichoic acids | ||||||
Function / homology | Lactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain / structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region / PHOSPHATE ION / S-layer protein Function and homology information | ||||||
Biological species | Lactobacillus acidophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Eder, M. / Dordic, A. / Sagmeister, T. / Vejzovic, D. / Pavkov-Keller, T. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: The molecular architecture of Lactobacillus S-layer: Assembly and attachment to teichoic acids. Authors: Sagmeister, T. / Gubensak, N. / Buhlheller, C. / Grininger, C. / Eder, M. / Ðordic, A. / Millan, C. / Medina, A. / Murcia, P.A.S. / Berni, F. / Hynonen, U. / Vejzovic, D. / Damisch, E. ...Authors: Sagmeister, T. / Gubensak, N. / Buhlheller, C. / Grininger, C. / Eder, M. / Ðordic, A. / Millan, C. / Medina, A. / Murcia, P.A.S. / Berni, F. / Hynonen, U. / Vejzovic, D. / Damisch, E. / Kulminskaya, N. / Petrowitsch, L. / Oberer, M. / Palva, A. / Malanovic, N. / Codee, J. / Keller, W. / Uson, I. / Pavkov-Keller, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8alu.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8alu.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 8alu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8alu_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8alu_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8alu_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 8alu_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/8alu ftp://data.pdbj.org/pub/pdb/validation_reports/al/8alu | HTTPS FTP |
-Related structure data
Related structure data | 7qecC 7qehSC 7qfgC 7qfiC 7qfjC 7qfkC 7qflC 7qldC 7qleC 7qlhC 8aolC 8bt9C 8q1oC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 14827.815 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: CXB72_00965 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A809K9V2 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: Index screen condition #80 (0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25 % PEG 3350) with a protein stock solution of 20 mg/mL in 20 mM ADA pH 6.5 and 100 mM NaCl. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→40.21 Å / Num. obs: 12330 / % possible obs: 84.51 % / Redundancy: 2.9 % / Biso Wilson estimate: 35.99 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.031 / Rrim(I) all: 0.056 / Net I/σ(I): 15.46 |
Reflection shell | Resolution: 2.09→2.17 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 340 / CC1/2: 0.751 / Rpim(I) all: 0.418 / Rrim(I) all: 0.7 / % possible all: 44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7QEH Resolution: 2.09→40.21 Å / SU ML: 0.3115 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.6413 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→40.21 Å
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Refine LS restraints |
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LS refinement shell |
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