+Open data
-Basic information
Entry | Database: PDB / ID: 5vga | ||||||
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Title | Alternative model for Fab 36-65 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / germline antibody anti-arsonate | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TRIETHYLENE GLYCOL Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Stanfield, R.L. / Rupp, B. / Wlodawer, A. / Dauter, Z. / Porebski, P.J. / Minor, W. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. | ||||||
Citation | Journal: Immunity / Year: 2006 Title: Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. Authors: Sethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M. | ||||||
History |
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Remark 0 | THIS ENTRY 5VGA REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN ENTRY 2A6I, DETERMINED BY ...THIS ENTRY 5VGA REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN ENTRY 2A6I, DETERMINED BY D.K.SETHI,A.AGARWAL,V.MANIVEL,K.V.RAO,D.M.SALUNKE" |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vga.cif.gz | 163.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vga.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/5vga ftp://data.pdbj.org/pub/pdb/validation_reports/vg/5vga | HTTPS FTP |
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-Related structure data
Related structure data | 5vehC 5vepC 5veqC 5verC 5vetC 5vf2C 5vf5C 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: 23707.049 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: 24135.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Chemical | ChemComp-PGE / |
#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: 2.52 Å3/Da / Density % sol: 51.3 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2A6I |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 16% PEG 8000, cacodylate, 0.05% azide |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 15724 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 1.7 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→23.453 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→23.453 Å
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Refine LS restraints |
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LS refinement shell |
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