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- PDB-1p7n: Dimeric Rous Sarcoma virus Capsid protein structure with an upstr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p7n | ||||||
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Title | Dimeric Rous Sarcoma virus Capsid protein structure with an upstream 25-amino acid residue extension of C-terminal of Gag p10 protein | ||||||
![]() | GAG POLYPROTEIN CAPSID PROTEIN P27 | ||||||
![]() | VIRAL PROTEIN / Retrovirus / capsid protein / Gag Polyprotein / immature gag | ||||||
Function / homology | ![]() host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / nucleic acid binding / structural constituent of virion / aspartic-type endopeptidase activity / host cell plasma membrane / proteolysis ...host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / nucleic acid binding / structural constituent of virion / aspartic-type endopeptidase activity / host cell plasma membrane / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nandhagopal, N. / Simpson, A.A. / Johnson, M.C. / Francisco, A.B. / Schatz, G.W. / Rossmann, M.G. / Vogt, V.M. | ||||||
![]() | ![]() Title: Dimeric rous sarcoma virus capsid protein structure relevant to immature gag assembly Authors: Nandhagopal, N. / Simpson, A.A. / Johnson, M.C. / Francisco, A.B. / Schatz, G.W. / Rossmann, M.G. / Vogt, V.M. | ||||||
History |
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Remark 999 | SEQUENCE The protein sequence contains the N-terminal domain of capsid protein P27 with an upstream ...SEQUENCE The protein sequence contains the N-terminal domain of capsid protein P27 with an upstream 25-amino acid extension C-terminal of GAG P10 PROTEIN. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.2 KB | Display | ![]() |
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PDB format | ![]() | 31.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.3 KB | Display | ![]() |
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Full document | ![]() | 429.2 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1em9S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18736.674 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.73 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 mM HEPES-sodium buffer and 0.8M potassium sodium tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. all: 7911 / Num. obs: 6743 / % possible obs: 85.2 % / Redundancy: 8.3 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.329 / Num. unique all: 396 / % possible all: 51.4 |
Reflection | *PLUS Redundancy: 3.18 % |
Reflection shell | *PLUS % possible obs: 51.4 % / Redundancy: 1.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EM9 Resolution: 2.6→26.5 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 558128.82 / Data cutoff high rms absF: 558128.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.5603 Å2 / ksol: 0.303224 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→26.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.26 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.366 / Rfactor Rwork: 0.337 |