[English] 日本語
Yorodumi- PDB-7qeh: LTA-binding domain of SlpA, the S-layer protein from Lactobacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qeh | ||||||
---|---|---|---|---|---|---|---|
Title | LTA-binding domain of SlpA, the S-layer protein from Lactobacillus amylovorus | ||||||
Components | S-layer | ||||||
Keywords | CELL ADHESION / s-layer / LTA-binding / lactobacillus amylovorus / polymer binding | ||||||
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 / PHOSPHATE ION / S-layer Function and homology information | ||||||
Biological species | Lactobacillus amylovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å | ||||||
Authors | Eder, M. / Dordic, A. / Sagmeister, T. / Pavkov-Keller, T. | ||||||
Funding support | Austria, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qeh.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qeh.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qeh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qeh_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qeh_full_validation.pdf.gz | 810 KB | Display | |
Data in XML | 7qeh_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 7qeh_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/7qeh ftp://data.pdbj.org/pub/pdb/validation_reports/qe/7qeh | HTTPS FTP |
-Related structure data
Related structure data | 7qecC 7qfgC 7qfiC 7qfjC 7qfkC 7qflC 7qldC 7qleC 7qlhC 8aluC 8aolC 8bt9C 8q1oC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16231.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus amylovorus (strain GRL 1112) (bacteria) Strain: GRL 1112 / Gene: LA2_00970 / Production host: Escherichia coli (E. coli) / References: UniProt: E4SK47 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.75 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Morpheus screen condition #2-29 (20 mM of each carboxylic acid (sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate, and sodium ...Details: Morpheus screen condition #2-29 (20 mM of each carboxylic acid (sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate, and sodium oxamate), 0.1 M sodium HEPES- MOPS pH 7.5 with 20 % v/v PEG 500 MME and 10 % w/v PEG 20000). A protein stock solution of 20 mg/mL in 10 mM HEPES pH 7 and 100 mM NaCl was used. 1uL drop with 1:1 ration protein to reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→39.08 Å / Num. obs: 26186 / % possible obs: 99.39 % / Redundancy: 12.2 % / Biso Wilson estimate: 18.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.114 / Net I/σ(I): 19.84 |
Reflection shell | Resolution: 1.67→1.734 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1361 / CC1/2: 0.805 / CC star: 0.947 / Rpim(I) all: 0.316 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.67→39.08 Å / SU ML: 0.1598 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8422 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→39.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|