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Open data
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Basic information
Entry | Database: PDB / ID: 4h0h | ||||||
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Title | Crystal structure of mimicry-recognizing 2D10 scFv with peptide | ||||||
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![]() | IMMUNE SYSTEM / molecular mimicry / sugar | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tapryal, S. / Gaur, V. / Kaur, K.J. / Salunke, D.M. | ||||||
![]() | ![]() Title: Structural evaluation of a mimicry-recognizing paratope: plasticity in antigen-antibody interactions manifests in molecular mimicry. Authors: Tapryal, S. / Gaur, V. / Kaur, K.J. / Salunke, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.9 KB | Display | ![]() |
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Full document | ![]() | 443.5 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h0gC ![]() 4h0iSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 26894.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1365.444 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, pH 6.5, 1.6 M magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 16, 2008 / Details: mirrors |
Radiation | Monochromator: Ni filter CMF 12 38CU-6 (Osmic Inc.) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→69.568 Å / Num. all: 19310 / Num. obs: 19310 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4H0I Resolution: 2→25.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.385 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE COORDINATES FOR RESIDUES 4-9 OF CHAIN D HAVE BEEN MODELED WHILE VISUALIZING THE 2FO-FC AND FO-FC MAPS AT SIGMA CUT-OFFS OF 0.7 AND 1.6, RESPECTIVELY, WITH AN OCCUPANCY OF 0.8 AND AN ...Details: THE COORDINATES FOR RESIDUES 4-9 OF CHAIN D HAVE BEEN MODELED WHILE VISUALIZING THE 2FO-FC AND FO-FC MAPS AT SIGMA CUT-OFFS OF 0.7 AND 1.6, RESPECTIVELY, WITH AN OCCUPANCY OF 0.8 AND AN AVERAGE B-FACTOR OF 92.1. THEREFORE, HIGHER REAL SPACE R-FACTORS AND LOWER DENSITY CORRELATION ARE EXPECTED FOR THESE RESIDUES.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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