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- PDB-2xxc: Crystal structure of a camelid VHH raised against the HIV-1 capsi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xxc | ||||||
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Title | Crystal structure of a camelid VHH raised against the HIV-1 capsid protein C-terminal domain. | ||||||
![]() | CAMELID VHH 9 | ||||||
![]() | IMMUNE SYSTEM | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
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 | ![]() | 40.5 KB | Display | ![]() |
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PDB format | ![]() | 27 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xt1SC ![]() 2xv6C ![]() 2xxmC 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
#1: Antibody | Mass: 13213.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | THE VHH RESIDUES (CHAIN B) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. THE 6XHISTIDINE TAG AT ...THE VHH RESIDUES (CHAIN B) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. THE 6XHISTIDINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.72 % / Description: NONE |
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Crystal grow | Details: 28-30 % W/V PEG 4000, 100 MM SODIUM CITRATE PH 4.6, 100 MM AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2009 Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→32 Å / Num. obs: 19028 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 25.32 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 58.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XT1 Resolution: 1.67→13.19 Å / Cor.coef. Fo:Fc: 0.9447 / Cor.coef. Fo:Fc free: 0.9249 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.085 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. THE 6XHISTIDINE TAG AT THE C-TERMINUS IS DISORDERED
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Displacement parameters | Biso mean: 30.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.183 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→13.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.76 Å / Total num. of bins used: 10
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