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- PDB-2uud: Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2uud | |||||||||
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Title | Crystal structure of the TEPC15-Vk45.1 anti-2-phenyl-5-oxazolone NQ10- 1.12 scFv in complex with the hapten | |||||||||
![]() | (NQ10-1.12 ANTI-PHOX ANTIBODY) x 3 | |||||||||
![]() | IMMUNE SYSTEM / SCFV / ANTIBODY / IMMUNOGLOBULIN / 2-PHENYL-5-OXAZOLONE / IMMUNOGLOBULIN DOMAIN | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-PHX![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Scotti, C. / Gherardi, E. | |||||||||
![]() | ![]() Title: Structural Basis of Affinity Maturation of the Tepc15-Vkappa45.1 Anti-2-Phenyl-5-Oxazolone Antibodies Authors: Scotti, C. / Gherardi, E. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.9 KB | Display | ![]() |
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PDB format | ![]() | 83 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cjuC ![]() 1flrS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Antibody | Mass: 13410.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 12423.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 1283.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.32 % |
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Crystal grow | pH: 7.6 Details: 0.1 M TRIS-HCL, PH 7.6, 0.2 M AMMONIUM SULPHATE, 30% PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 13, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→65.64 Å / Num. obs: 11988 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 75.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.22 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FLR Resolution: 2.9→19.9 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 809326.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: FOR REFINEMENT-REBUILDING, THE PROGRAM LAFIRE HAS BEEN USED, STARTING FROM THE 2CJV STRUCTURE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.3383 Å2 / ksol: 0.336356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.99 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 11
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Xplor file |
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