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Yorodumi- PDB-4b41: Crystal structure of an amyloid-beta binding single chain antibody G7 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b41 | ||||||
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Title | Crystal structure of an amyloid-beta binding single chain antibody G7 | ||||||
Components | ANTIBODY G7 | ||||||
Keywords | IMMUNE SYSTEM / ALZHEIMER'S DISEASE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | LAMA GLAMA (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.191 Å | ||||||
Authors | Beringer, D.X. / Dorresteijn, B. / Rutten, L. / Wienk, H. / el Khattabi, M. / Kroon-Batenburg, L.M.J. / Verrips, C.T. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of an Amyloid-Beta Binding Single Chain Antibody G7 Authors: Beringer, D.X. / Dorresteijn, B. / Rutten, L. / Wienk, H. / El Khattabi, M. / Kroon-Batenburg, L.M.J. / Verrips, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b41.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b41.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 4b41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/4b41 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/4b41 | HTTPS FTP |
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-Related structure data
Related structure data | 3ezjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 12667.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMEK220 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.6 % / Description: NONE |
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Crystal grow | pH: 5.2 / Details: 0.1 M NA CITRATE PH 5.2, 0.2 NACL, 26-30% PEG8K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2010 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→49.94 Å / Num. obs: 50156 / % possible obs: 85.1 % / Observed criterion σ(I): 6.7 / Redundancy: 3.4 % / Biso Wilson estimate: 10.26 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.19→1.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.7 / % possible all: 62.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EZJ Resolution: 1.191→49.936 Å / SU ML: 0.09 / σ(F): 1.96 / Phase error: 18.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.191→49.936 Å
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Refine LS restraints |
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LS refinement shell |
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