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Yorodumi- PDB-7qld: Crystal structure of S-layer protein SlpA from Lactobacillus acid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qld | ||||||
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Title | Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I, Co-crystallization with HgCl2, Mutation Ser146Cys, (aa 32-198) | ||||||
Components | S-layer protein | ||||||
Keywords | STRUCTURAL PROTEIN / SlpA / Surface Layer Protein / S-layer / self-assembly / Lactobacillus acidophilus | ||||||
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 / extracellular region / : / S-layer protein Function and homology information | ||||||
Biological species | Lactobacillus acidophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.153 Å | ||||||
Authors | Sagmeister, T. / Vejzovic, D. / Eder, M. / Dordic, A. / 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 | 7qld.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qld.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qld_validation.pdf.gz | 602.2 KB | Display | wwPDB validaton report |
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Full document | 7qld_full_validation.pdf.gz | 603.3 KB | Display | |
Data in XML | 7qld_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 7qld_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/7qld ftp://data.pdbj.org/pub/pdb/validation_reports/ql/7qld | HTTPS FTP |
-Related structure data
Related structure data | 7qecC 7qehC 7qfgC 7qfiC 7qfjC 7qfkC 7qflC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 30 - 193 / Label seq-ID: 2 - 165
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 17259.670 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with ...Details: Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop and co-crystallization with 0.1 ul 2mM HgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.15→48.38 Å / Num. obs: 23300 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Net I/σ(I): 25 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.153→48.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.377 / SU ML: 0.156 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.189 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: 65.442 Å2
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Refinement step | Cycle: LAST / Resolution: 2.153→48.38 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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