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Yorodumi- PDB-7qlh: Crystal structure of S-layer protein SlpA from Lactobacillus amyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qlh | ||||||
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Title | Crystal structure of S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa 48-213) | ||||||
Components | S-layer | ||||||
Keywords | STRUCTURAL PROTEIN / s-layer / surface layer / bacterial / lactobacillus amylovorus / SlpA / self-assembly | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Grininger, C. / Sagmeister, T. / Eder, E. / 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 | 7qlh.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qlh.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qlh_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 7qlh_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 7qlh_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 7qlh_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/7qlh ftp://data.pdbj.org/pub/pdb/validation_reports/ql/7qlh | HTTPS FTP |
-Related structure data
Related structure data | 7qecC 7qehC 7qfgC 7qfiC 7qfjC 7qfkC 7qflC 7qldC 7qleSC 8aluC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18885.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus amylovorus (bacteria) / Strain: GRL 1112 / Gene: LA2_00970 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: E4SK47 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystallization condition 0.1 M MES, 40 % v/v MPD, 5 % w/v PEG 8000 Protein solution 20 mg/ml in 20 mM HEPES pH 8.0, 100 mM NaCl Setup 0.5 ul crystallization condition + 0.5 ul protein solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9429 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9429 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.79 Å / Num. obs: 19468 / % possible obs: 99.02 % / Redundancy: 6.3 % / Biso Wilson estimate: 45.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05662 / Net I/σ(I): 19.32 |
Reflection shell | Resolution: 2.3→2.382 Å / Rmerge(I) obs: 0.4732 / Mean I/σ(I) obs: 4.17 / Num. unique obs: 1908 / CC1/2: 0.959 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7QLE Resolution: 2.3→43.79 Å / SU ML: 0.2691 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7997 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: 55.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.79 Å
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Refine LS restraints |
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LS refinement shell |
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