+Open data
-Basic information
Entry | Database: PDB / ID: 3o6l | ||||||
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Title | Anti-Tat HIV 11H6H1 Fab' complexed with a 15-mer Tat peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antigen-binding site / U-shaped groove / Tat HIV | ||||||
Function / homology | Function and homology information positive regulation of viral transcription / host cell nucleolus / RNA-binding transcription regulator activity / molecular adaptor activity / RNA binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Serriere, J. / Gouet, P. / Guillon, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Fab'-induced folding of antigenic N-terminal peptides from intrinsically disordered HIV-1 Tat revealed by X-ray crystallography. Authors: Serriere, J. / Dugua, J.M. / Bossus, M. / Verrier, B. / Haser, R. / Gouet, P. / Guillon, C. #1: Journal: Proteins / Year: 2010 Title: UV and X-ray structural studies of a 101-residue long Tat protein from a HIV-1 primary isolate and of its mutated, detoxified, vaccine candidate Authors: Foucault, M. / Mayol, K. / Receveur-Brechot, V. / Bussat, M.C. / Klinguer-Hamour, C. / Verrier, B. / Beck, A. / Haser, R. / Gouet, P. / Guillon, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o6l.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o6l.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 3o6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/3o6l ftp://data.pdbj.org/pub/pdb/validation_reports/o6/3o6l | HTTPS FTP |
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-Related structure data
Related structure data | 3o6kC 3o6mC 1mlbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24219.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C |
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#2: Antibody | Mass: 23553.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C |
#3: Protein/peptide | Mass: 1718.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized / References: UniProt: Q98XH7 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 289 K / Method: soaking / pH: 6.5 Details: 0.05M CaCl2, 0.1M Bis-Tris pH 6.5, 30% (v/v) polyethylene glycol 550 monomethyl ether, Soaking of Fab' crystals with 0.1mM Tat-peptide for 1 hour, then 0.5mM for 2 hours, soaking, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97941 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97941 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 28645 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.14 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.73 / Num. unique all: 604 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MLB Resolution: 2.1→19.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.681 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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