+Open data
-Basic information
Entry | Database: PDB / ID: 2g75 | ||||||
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Title | Crystal Structure of anti-SARS m396 Antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / SARS / S protein / antibody / epitopes / vaccines / inhibitors | ||||||
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: 2.28 Å | ||||||
Authors | Prabakaran, P. / Gan, J.H. / Feng, Y. / Zhu, Z.Y. / Xiao, X.D. / Ji, X. / Dimitrov, D.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody. Authors: Prabakaran, P. / Gan, J. / Feng, Y. / Zhu, Z. / Choudhry, V. / Xiao, X. / Ji, X. / Dimitrov, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g75.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g75.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 2g75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g75_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 2g75_full_validation.pdf.gz | 478.2 KB | Display | |
Data in XML | 2g75_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 2g75_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g75 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g75 | HTTPS FTP |
-Related structure data
Related structure data | 2dd8SC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25979.938 Da / Num. of mol.: 2 / Fragment: Fab m396, Heavy Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: recombinant antibody Fab / Plasmid: pDZ1.0 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 #2: Antibody | Mass: 22807.094 Da / Num. of mol.: 2 / Fragment: Fab m396, Light Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: recombinant antibody Fab / Plasmid: pDZ1.0 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 #3: 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: 2.35 Å3/Da / Density % sol: 47.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% v/v Glycerol, 16% v/v Ethylene Glycol, 20% w/v PEG 6000, and 100 mM NaCl in 30 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: Oct 14, 2005 / Details: Mirror |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→29.91 Å / Num. all: 34411 / Num. obs: 34411 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.28→2.37 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1950 / % possible all: 42.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DD8 Resolution: 2.28→29.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 334072.45 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0599 Å2 / ksol: 0.344674 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.42 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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