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Yorodumi- PDB-2jsv: Dipole tensor-based refinement for atomic-resolution structure de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jsv | ||||||
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Title | Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | IMMUNE SYSTEM / SSNMR / GB1 / tensor refinement / Cell wall / IgG-binding protein / Peptidoglycan-anchor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sp. 'group G' (bacteria) | ||||||
Method | SOLID-STATE NMR / DGSA-distance geometry simulated annealing, simulated annealing | ||||||
Authors | Franks, W. / Wylie, B.J. / Frericks, H.L. / Nieuwkoop, A.J. / Mayrhofer, R. / Shah, G.J. / Graesser, D.T. / Rienstra, C.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR Authors: Franks, W.T. / Wylie, B.J. / Schmidt, H.L. / Nieuwkoop, A.J. / Mayrhofer, R.M. / Shah, G.J. / Graesser, D.T. / Rienstra, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jsv.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jsv.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jsv_validation.pdf.gz | 342.9 KB | Display | wwPDB validaton report |
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Full document | 2jsv_full_validation.pdf.gz | 417.1 KB | Display | |
Data in XML | 2jsv_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 2jsv_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/2jsv ftp://data.pdbj.org/pub/pdb/validation_reports/js/2jsv | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 6228.809 Da / Num. of mol.: 1 / Fragment: 2-1 repeat / Mutation: T2Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909 |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR / Details: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The precipitant was packed with excess mother liquor for data acquisition. |
-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 5.5 / Pressure: ambient / Temperature: 281 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, simulated annealing Software ordinal: 1 Details: 50,000 steps at 2500 K, decreased over 25,000 steps to 1000 K, 1 fs step size, 70,000 steps from 1000K to 300 K, 1 fs step size | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 260 / Conformers submitted total number: 10 |