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- PDB-2xt1: Crystal structure of the HIV-1 capsid protein C-terminal domain (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xt1 | ||||||
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Title | Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 231) in complex with a camelid VHH. | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Igonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A. | ||||||
![]() | ![]() Title: Targeting HIV-1 Virion Formation with Nanobodies -Implications for the Design of Assembly Inhibitors Authors: Igonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.1 KB | Display | ![]() |
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PDB format | ![]() | 42.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.8 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xv6C ![]() 2xxcC ![]() 2xxmC ![]() 1kxvS ![]() 2buoS C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 9530.921 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 146-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Antibody | Mass: 13213.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE VHH RESIDUES (CHAIN B) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % / Description: NONE |
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Crystal grow | Details: 28-32 % W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→44.1 Å / Num. obs: 45032 / % possible obs: 98.2 % / Observed criterion σ(I): 2.1 / Redundancy: 13.7 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.32→1.39 Å / Redundancy: 5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 88.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2BUO, 1KXV Resolution: 1.32→35.54 Å / Cor.coef. Fo:Fc: 0.9647 / Cor.coef. Fo:Fc free: 0.9558 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.053 / SU Rfree Cruickshank DPI: 0.05 Details: THE 6XHISTIDINE TAG AT THE C-TERMINAL END OF CHAIN B IS DISORDERED.
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Displacement parameters | Biso mean: 15.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.129 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→35.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.35 Å / Total num. of bins used: 20
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