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Yorodumi- PDB-1tzg: Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tzg | ||||||
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Title | Crystal structure of HIV-1 neutralizing human Fab 4E10 in complex with a 13-residue peptide containing the 4E10 epitope on gp41 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody-epitope complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cardoso, R.M.F. / Zwick, M.B. / Stanfield, R.L. / Kunert, R. / Binley, J.M. / Katinger, H. / Burton, D.R. / Wilson, I.A. | ||||||
Citation | Journal: Immunity / Year: 2005 Title: Broadly Neutralizing Anti-HIV Antibody 4E10 Recognizes a Helical Conformation of a Highly Conserved Fusion-Associated Motif in gp41 Authors: Cardoso, R.M.F. / Zwick, M.B. / Stanfield, R.L. / Kunert, R. / Binley, J.M. / Katinger, H. / Burton, D.R. / Wilson, I.A. | ||||||
History |
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Remark 999 | SEQUENCE A suitable database reference sequence could not be found for the protein chains in this ...SEQUENCE A suitable database reference sequence could not be found for the protein chains in this structure at the time of processing |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tzg.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tzg.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tzg ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tzg | HTTPS FTP |
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-Related structure data
Related structure data | 1hklS 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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2 |
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3 |
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Unit cell |
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Details | The asymmetric unit contains two biological units (2 Fab-peptide complexes) |
-Components
#1: Antibody | Mass: 23292.705 Da / Num. of mol.: 2 / Fragment: light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 24424.518 Da / Num. of mol.: 2 / Fragment: heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) #3: Protein/peptide | Mass: 1653.837 Da / Num. of mol.: 2 / Fragment: Transmembrane glycoprotein / Source method: obtained synthetically #4: Chemical | #5: 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: 3.26 Å3/Da / Density % sol: 62.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG 8000, sodium acetate, hexamine cobalt trichloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979126 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2003 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979126 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 61572 / % possible obs: 93 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4037 / Rsym value: 0.371 / % possible all: 61.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HKL Resolution: 2.2→43 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 42.178 Å2 / ksol: 0.329003 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014
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Xplor file |
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