+Open data
-Basic information
Entry | Database: PDB / ID: 3cle | ||||||
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Title | HIV neutralizing monoclonal antibody YZ23 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / monoclonal antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Jin, L. / Paul, S. / Symersky, J. | ||||||
Citation | Journal: To be Published Title: HIV neutralizing monoclonal antibody YZ23 Authors: Nishiama, Y. / Planque, S. / Mitsuda, Y. / Taguchi, H. / Jin, L. / Symersky, J. / Boivin, S. / Salas, M. / Hanson, C. / Paul, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cle.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cle.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cle_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 3cle_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 3cle_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3cle_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/3cle ftp://data.pdbj.org/pub/pdb/validation_reports/cl/3cle | HTTPS FTP |
-Related structure data
Related structure data | 3clfC 1kn2S S: Starting model for refinement 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: 23678.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: hybridoma |
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#2: Antibody | Mass: 23473.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: hybridoma |
#3: 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: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 16% PEG6000, 0.1 M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.5 Å / Num. all: 16453 / Num. obs: 15906 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.11 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KN2 Resolution: 2.5→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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