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Open data
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Basic information
Entry | Database: PDB / ID: 1p4i | ||||||
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Title | Crystal Structure of scFv against peptide GCN4 | ||||||
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![]() | IMMUNE SYSTEM / peptide binder / scFv / picomolar binder | ||||||
Function / homology | ![]() immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / blood microparticle / immune response / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zahnd, C. / Spinelli, S. / Luginbuhl, B. / Jermutus, L. / Amstutz, P. / Cambillau, C. / Pluckthun, A. | ||||||
![]() | ![]() Title: Directed in Vitro Evolution and Crystallographic Analysis of a Peptide-binding Single Chain Antibody Fragment (scFv) with Low Picomolar Affinity. Authors: Zahnd, C. / Spinelli, S. / Amstutz, P. / Cambillau, C. / Pluckthun, A. | ||||||
History |
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Remark 999 | SEQUENCE an appropriate sequence database reference for chains L and H were not available at the ...SEQUENCE an appropriate sequence database reference for chains L and H were not available at the time of processing. The author states that the sequence has not been deposited in any sequence database. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.4 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438 KB | Display | ![]() |
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Full document | ![]() | 445.4 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p4bC ![]() 1mfaS 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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Unit cell |
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Components
#1: Antibody | Mass: 13333.484 Da / Num. of mol.: 1 / Mutation: N36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 13447.799 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: ammonium sulfate, sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→24 Å / Num. obs: 6870 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.28 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MFA Resolution: 2.8→12 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→12 Å
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