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Yorodumi- PDB-8q1o: S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q1o | ||||||
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Title | S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa 32-209), important for Self-assembly | ||||||
Components | S-layer | ||||||
Keywords | STRUCTURAL PROTEIN / Self assembly / S-layer | ||||||
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: 3.401 Å | ||||||
Authors | Sagmeister, T. / Grininger, C. / Eder, M. / 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 | 8q1o.cif.gz | 140.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q1o.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 8q1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q1o_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 8q1o_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 8q1o_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 8q1o_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/8q1o ftp://data.pdbj.org/pub/pdb/validation_reports/q1/8q1o | HTTPS FTP |
-Related structure data
Related structure data | 7qecC 7qehC 7qfgC 7qfiC 7qfjC 7qfkC 7qflC 7qldC 7qleC 7qlhC 8aluC 8aolC 8bt9C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 32 - 209 / Label seq-ID: 1 - 178
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 19392.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus amylovorus (bacteria) / Gene: LA2_00970 / Production host: Escherichia coli (E. coli) / References: UniProt: E4SK47 #2: Chemical | #3: 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: 3.24 Å3/Da / Density % sol: 62.01 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Condition: 1.0 M Ammonium formate, 0.1 M Sodium acetate pH 5.0, 8 % w/v PGA with protein end concentration of 7.5 ...Details: Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Condition: 1.0 M Ammonium formate, 0.1 M Sodium acetate pH 5.0, 8 % w/v PGA with protein end concentration of 7.5 mg/mL corresponding to 50% of protein solution in the 1.0 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: 1.0047 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0047 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.4→42.993 Å / Num. obs: 7031 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.191 / Rrim(I) all: 0.278 / Net I/σ(I): 5.2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.401→42.993 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.835 / SU B: 53.987 / SU ML: 0.767 / Cross valid method: FREE R-VALUE / ESU R Free: 0.731 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: 74.477 Å2
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Refinement step | Cycle: LAST / Resolution: 3.401→42.993 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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