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- PDB-1jpx: Mutation that destabilize the gp41 core: determinants for stabili... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jpx | ||||||
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Title | Mutation that destabilize the gp41 core: determinants for stabilizing the SIV/CPmac envelope glycoprotein complex. Wild type. | ||||||
![]() | gp41 envelope protein | ||||||
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Function / homology | ![]() membrane fusion involved in viral entry into host cell / host cell endosome membrane / membrane => GO:0016020 / symbiont entry into host cell / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J. / Wang, S. / LaBranche, C.C. / Hoxie, J.A. / Lu, M. | ||||||
![]() | ![]() Title: Mutations that destabilize the gp41 core are determinants for stabilizing the simian immunodeficiency virus-CPmac envelope glycoprotein complex. Authors: Liu, J. / Wang, S. / Hoxie, J.A. / LaBranche, C.C. / Lu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.4 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jq0C ![]() 1qbzS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | The biological assembly is a trimer generated from each of the three monomers by the three fold axis. |
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Components
#1: Protein | Mass: 9863.165 Da / Num. of mol.: 3 / Fragment: N40(L6)C38 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.42 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Sodium chloride, CTAB, barium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→50 Å / Num. all: 9729 / Num. obs: 9729 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1003 / % possible all: 94 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 129420 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Rmerge(I) obs: 0.209 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1QBZ Resolution: 2.3→44.77 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 469445.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 112.528 Å2 / ksol: 0.354022 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→44.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor obs: 0.237 / Rfactor Rfree![]() ![]() | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.357 / Rfactor Rwork: 0.301 |