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- PDB-2b1h: Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2b1h | ||||||
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Title | Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG29 peptide | ||||||
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![]() | IMMUNE SYSTEM / Fab-peptide complex / HIV-1 / gp120 / v3 loop | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stanfield, R.L. / Gorny, M.K. / Zolla-Pazner, S. / Wilson, I.A. | ||||||
![]() | ![]() Title: Crystal structures of human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 2219 in complex with three different V3 peptides reveal a new binding mode for HIV-1 cross-reactivity. Authors: Stanfield, R.L. / Gorny, M.K. / Zolla-Pazner, S. / Wilson, I.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.5 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.1 KB | Display | ![]() |
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Full document | ![]() | 454.7 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b0sSC ![]() 2b1aC 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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Unit cell |
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Components
#1: Antibody | Mass: 22949.303 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Antibody | Mass: 24155.715 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein/peptide | Mass: 2596.017 Da / Num. of mol.: 1 / Fragment: residues 96-118 / Source method: obtained synthetically Details: This sequence occurs in Human immunodeficiency virus type 1 (isolate MN) References: GenBank: 50982993 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 25% MPEG 5000, 0.2M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→67.42 Å / Num. all: 39609 / Num. obs: 39609 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 33.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1963 / Rsym value: 0.612 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2B0S Resolution: 2→67.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.471 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.15 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.055 Å2
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Refinement step | Cycle: LAST / Resolution: 2→67.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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