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Yorodumi- PDB-4h20: Crystal Structure and Computational Modeling of the Fab Fragment ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h20 | ||||||
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Title | Crystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig / Anti Ricin Antibody Fab fragment / Ricin A chain / extracellular / bloodstream | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhao, Z. / Worthylake, D.K. / LeCour Jr., L.F. / Maresh, G. / Pincus, S.H. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody. Authors: Zhao, Z. / Worthylake, D. / Lecour, L. / Maresh, G.A. / Pincus, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h20.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h20.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 4h20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h20_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 4h20_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 4h20_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4h20_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/4h20 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/4h20 | HTTPS FTP |
-Related 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: 23630.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23427.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#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: 2.35 Å3/Da / Density % sol: 47.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.4 Details: 25 mM NaCl, 10 mM Tris-HCl (pH 7.4),1 mM EDTA, 95-98 mM lithium nitrate, 20% w/v PEG 3350, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 19, 2011 / Details: Helios |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→14.8 Å / Num. all: 34728 / Num. obs: 34728 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 5.6 Å2 / Rsym value: 4.28 / Net I/σ(I): 22.67 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 7.68 / Num. unique all: 4383 / Rsym value: 9.34 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3DIF chain A, PDB ID 1EGJ chain H Resolution: 1.9→14.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→14.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013
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