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- PDB-2y07: CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3-NITROPHENYL) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y07 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3-NITROPHENYL) - ACETYL MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3 FAB FRAGMENT IN COMPLEX WITH A PHAGE DISPLAY DERIVED DODECAPEPTIDE PPYPAWHAPGNI | ||||||
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![]() | IMMUNE SYSTEM / BETA-SANDWICH IMMUNOGLOBULIN FOLD / ANTIGEN BINDING / SECRETED PROTEIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Khan, T. / Salunke, D.M. | ||||||
![]() | ![]() Title: Structural Elucidation of the Mechanistic Basis of Degeneracy in the Primary Humoral Response. Authors: Khan, T. / 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 | ![]() | 96.6 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 471.5 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 23458.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 22538.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein/peptide | Mass: 1320.473 Da / Num. of mol.: 1 / Fragment: PEPTIDE, RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.2 % / Description: NONE |
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Crystal grow | pH: 7.1 Details: 50 MM TRIS HCL, 0.025% SODIUM AZIDE, PEG 3350, pH 7.1 |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2008 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER CMF12 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: 2.4→23.62 Å / Num. obs: 14326 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.6 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NATIVE FAB STRUCTURE Resolution: 2.4→23.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 184279.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.8733 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→23.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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