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Yorodumi- PDB-7wio: NMR structure of N-terminal domain of Triconephila clavipes of ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wio | |||||||||
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Title | NMR structure of N-terminal domain of Triconephila clavipes of major ampullate spidroin 1 | |||||||||
Components | Major ampullate spidroin 1A | |||||||||
Keywords | STRUCTURAL PROTEIN / Dragline spider silk / spider silk assembly / pH regulation | |||||||||
Function / homology | Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Major ampullate spidroin 1A Function and homology information | |||||||||
Biological species | Trichonephila clavipes (spider) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Oktaviani, N.A. / Malay, A.D. / Matsugami, A. / Hayashi, F. / Numata, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biomacromolecules / Year: 2023 Title: Unusual p K a Values Mediate the Self-Assembly of Spider Dragline Silk Proteins. Authors: Oktaviani, N.A. / Malay, A.D. / Matsugami, A. / Hayashi, F. / Numata, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wio.cif.gz | 763.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wio.ent.gz | 640.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wio_validation.pdf.gz | 402.7 KB | Display | wwPDB validaton report |
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Full document | 7wio_full_validation.pdf.gz | 522.5 KB | Display | |
Data in XML | 7wio_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 7wio_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/7wio ftp://data.pdbj.org/pub/pdb/validation_reports/wi/7wio | HTTPS FTP |
-Related structure data
Related structure data | 8gs7C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14498.997 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichonephila clavipes (spider) / Gene: MaSp1A / Production host: Escherichia coli (E. coli) / References: UniProt: B5SYS5 |
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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: fibrous protein Contents: 1 mM [U-13C; U-15N] N-terminal domain of Triconephila clavipes of major ampullate spidroin 1, 0.1 mM DSS, 10 % v/v [U-100% 2H] D2O, 300 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O Label: 13C_15N NTD MaSp1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 300 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 5 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |