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Yorodumi- PDB-7qfl: Crystal structure of S-layer protein SlpA from Lactobacillus acid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qfl | ||||||
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Title | Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain II (aa 199-308) | ||||||
Components | S-layer protein | ||||||
Keywords | STRUCTURAL PROTEIN / s-layer / surface layer / bacterial / lactobacillus acidophilus / SlpA / self-assembly | ||||||
Function / homology | Function and homology information structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / extracellular region Similarity search - Function | ||||||
Biological species | Lactobacillus acidophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Sagmeister, T. / Dordic, A. / Eder, E. / 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 | 7qfl.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qfl.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qfl_validation.pdf.gz | 897.9 KB | Display | wwPDB validaton report |
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Full document | 7qfl_full_validation.pdf.gz | 897.9 KB | Display | |
Data in XML | 7qfl_validation.xml.gz | 7 KB | Display | |
Data in CIF | 7qfl_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/7qfl ftp://data.pdbj.org/pub/pdb/validation_reports/qf/7qfl | HTTPS FTP |
-Related structure data
Related structure data | 7qecSC 7qehC 7qfgC 7qfiC 7qfjC 7qfkC 7qldC 7qleC 7qlhC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14158.630 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: slpA, LBA0169 / Production host: Escherichia coli (E. coli) / References: UniProt: P35829 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: protein stock solution of 18.5 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 1-1 (0.18 M lithium sulfate, 90 mM sodium acetate pH 4.5 and 45 % w/v PEG 400) with protein ...Details: protein stock solution of 18.5 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 1-1 (0.18 M lithium sulfate, 90 mM sodium acetate pH 4.5 and 45 % w/v PEG 400) with protein end concentration of 12.3 mg/mL corresponding to 66.67 % of protein solution in the 1.5 uL drop. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.37 Å / Num. obs: 23163 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.042 / Rrim(I) all: 0.095 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.85 / Num. unique obs: 21345 / CC1/2: 0.821 / Rpim(I) all: 0.427 / Rrim(I) all: 0.953 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7QEC Resolution: 1.4→48.368 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.836 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.057 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.088 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→48.368 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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