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Yorodumi- PDB-7qec: Crystal structure of SlpA - domain II, domain that is involved in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qec | ||||||
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Title | Crystal structure of SlpA - domain II, domain that is involved in the self-assembly of the S-layer from Lactobacillus amylovorus | ||||||
Components | S-layer | ||||||
Keywords | STRUCTURAL PROTEIN / s-layer / self-assembly / lactobacillus amylovorus | ||||||
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 / S-layer Function and homology information | ||||||
Biological species | Lactobacillus amylovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.95 Å | ||||||
Authors | Eder, M. / Dordic, A. / Millan, C. / Sagmeister, T. / Uson, I. / 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 | 7qec.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qec.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qec_validation.pdf.gz | 418.5 KB | Display | wwPDB validaton report |
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Full document | 7qec_full_validation.pdf.gz | 418.5 KB | Display | |
Data in XML | 7qec_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 7qec_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/7qec ftp://data.pdbj.org/pub/pdb/validation_reports/qe/7qec | HTTPS FTP |
-Related structure data
Related structure data | 7qehC 7qfgC 7qfiC 7qfjC 7qfkC 7qflC 7qldC 7qleC 7qlhC 8aluC 8aolC 8bt9C 8q1oC 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: 11641.812 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Morpheus screen condition #1-24 (30 mM of each halogen (sodium fluoride, sodium bromide and sodium iodide), 0.1 M Bicine/Trizma base pH 8.5 with 12.5% v/v MPD, 12.5 % PEG 1000 and 12.5 % w/v ...Details: Morpheus screen condition #1-24 (30 mM of each halogen (sodium fluoride, sodium bromide and sodium iodide), 0.1 M Bicine/Trizma base pH 8.5 with 12.5% v/v MPD, 12.5 % PEG 1000 and 12.5 % w/v PEG 3350). Protein stock solution of 4.18 mg/mL in 10 mM Hepes pH 7 and 50 mM NaCl. Drops: 0.5 + 0.5uL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35.61 Å / Num. obs: 14655 / % possible obs: 98.13 % / Redundancy: 18.9 % / Biso Wilson estimate: 33.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.026 / Rrim(I) all: 0.118 / Net I/σ(I): 17.79 |
Reflection shell | Resolution: 1.951→2.021 Å / Rmerge(I) obs: 0.9 / Num. unique obs: 682 / CC1/2: 0.759 / Rpim(I) all: 0.244 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.95→35.61 Å / SU ML: 0.2341 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9081 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: 37.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→35.61 Å
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Refine LS restraints |
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LS refinement shell |
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