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Yorodumi- PDB-3idi: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3idi | ||||||
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Title | Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide ALDKWNQ | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / gp41 / MPER / 2F5 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Julien, J.-P. / Bryson, S. / Pai, E.F. | ||||||
Citation | Journal: J.Virol. / Year: 2009 Title: Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications. Authors: Bryson, S. / Julien, J.P. / Hynes, R.C. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3idi.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3idi.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 3idi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3idi ftp://data.pdbj.org/pub/pdb/validation_reports/id/3idi | HTTPS FTP |
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-Related structure data
Related structure data | 1u8hC 1u8iC 1u8jC 1u8lC 1u8mC 1u8nC 1u8oC 1u8pC 1u8qC 1u91C 1u92C 1u93C 1u95C 2f5aC 2f5bC 2pw1C 2pw2C 3idgC 3idjC 3idmC 3idnC C: citing same article (ref.) |
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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
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 874.960 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 25245.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-Non-polymers , 3 types, 212 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M sodium citrate, pH 5.6, 16% 2-propanol, 16% PEG 4000, 0.1% Tween-20, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 16, 2008 |
Radiation | Monochromator: Rigaku optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 27454 / Num. obs: 25395 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.392 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1041152.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.488 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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