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Yorodumi- PDB-3idg: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3idg | ||||||
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Title | Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide ALDKWD | ||||||
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 / Resolution: 1.86 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 | 3idg.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3idg.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 3idg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3idg ftp://data.pdbj.org/pub/pdb/validation_reports/id/3idg | 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 3idiC 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
#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) |
#3: Protein/peptide | Mass: 747.816 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 3.35 Å3/Da / Density % sol: 63.25 % |
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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, 1.4 M ammonium sulfate, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 19, 2001 |
Radiation | Monochromator: Xenox mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→20 Å / Num. all: 56568 / Num. obs: 53513 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.042 |
Reflection shell | Resolution: 1.86→1.98 Å / Rsym value: 0.341 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Resolution: 1.86→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 717428.74 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.6718 Å2 / ksol: 0.382229 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.86→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.86→1.98 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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