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Yorodumi- PDB-2kgf: N-terminal domain of capsid protein from the Mason-Pfizer monkey virus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kgf | ||||||
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Title | N-terminal domain of capsid protein from the Mason-Pfizer monkey virus | ||||||
Components | Capsid protein p27 | ||||||
Keywords | VIRAL PROTEIN / Retrovirus capsid protein / N-terminal core domain (SCOP) / Capsid protein | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / nucleic acid binding / structural constituent of virion / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mason-Pfizer monkey virus | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Macek, P. / Chmelik, J. / Zidek, L. / Kaderavek, P. / Padrta, P. / Ruml, T. / Pichova, I. / Rumlova, M. / Sklenar, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: NMR structure of the N-terminal domain of capsid protein from the mason-pfizer monkey virus Authors: Macek, P. / Chmelik, J. / Krizova, I. / Kaderavek, P. / Padrta, P. / Zidek, L. / Wildova, M. / Hadravova, R. / Chaloupkova, R. / Pichova, I. / Ruml, T. / Rumlova, M. / Sklenar, V. #1: Journal: Biomol.Nmr Assign. / Year: 2008 Title: 1H, 13C, and 15N resonance assignment of the N-terminal domain of Mason-Pfizer monkey virus capsid protein, CA 1-140 Authors: Macek, P. / Zidek, L. / Rumlova, M. / Pichova, I. / Sklenar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kgf.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kgf.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 2kgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/2kgf ftp://data.pdbj.org/pub/pdb/validation_reports/kg/2kgf | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 15470.034 Da / Num. of mol.: 1 / Fragment: UNP residues 300-439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mason-Pfizer monkey virus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07567 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 150mM NaCl / pH: 8 / Pressure: ambient / Temperature: 295 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR constraints | NOE constraints total: 2246 / NOE intraresidue total count: 836 / NOE long range total count: 445 / NOE medium range total count: 450 / NOE sequential total count: 515 / Hydrogen bond constraints total count: 124 / Protein phi angle constraints total count: 107 / Protein psi angle constraints total count: 107 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: 10 structures for lowest energy Conformers calculated total number: 150 / Conformers submitted total number: 50 / Representative conformer: 1 |