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Yorodumi- PDB-6zso: Solution structure of the water-soluble LU-domain of human Lypd6b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zso | ||||||
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Title | Solution structure of the water-soluble LU-domain of human Lypd6b protein | ||||||
Components | Ly6/PLAUR domain-containing protein 6B | ||||||
Keywords | NEUROPEPTIDE / Lypd6b / Ly6/uPAR / nicotinic acetylcholine receptor modulator / three-finger proteins | ||||||
Function / homology | Ly6/PLAUR domain-containing protein 6-like / acetylcholine receptor regulator activity / : / Post-translational modification: synthesis of GPI-anchored proteins / extracellular region / plasma membrane / Ly6/PLAUR domain-containing protein 6B Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Tsarev, A.V. / Kulbatskii, D.S. / Paramonov, A.S. / Lyukmanova, E.N. / Shenkarev, Z.O. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2020 Title: Structural Diversity and Dynamics of Human Three-Finger Proteins Acting on Nicotinic Acetylcholine Receptors. Authors: Paramonov, A.S. / Kocharovskaya, M.V. / Tsarev, A.V. / Kulbatskii, D.S. / Loktyushov, E.V. / Shulepko, M.A. / Kirpichnikov, M.P. / Lyukmanova, E.N. / Shenkarev, Z.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zso.cif.gz | 558 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zso.ent.gz | 480.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zso ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zso | HTTPS FTP |
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-Related structure data
Related structure data | 6ib6C 6zssC 6zzeC 6zzfC C: citing same article (ref.) |
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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: Protein | Mass: 11012.296 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LYPD6B / Plasmid: pET22b(+) Details (production host): coding sequence cloned into pET22b(+) between NdeI and HindIII sites Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NI32 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 0.2 mM [U-13C; U-15N] lypd6, 95% H2O/5% D2O / Label: lypd6bCN / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 0.2 mM / Component: lypd6 / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Ionic strength: 10 mM / Ionic strength err: 5 / Label: sol1 / pH: 5.5 / PH err: 0.05 / Pressure: AMBIENT Pa / Temperature: 303 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 3 | ||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 |