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- PDB-4aix: Crystallographic structure of an amyloidogenic variant, 3rC34Y, o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aix | ||||||
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Title | Crystallographic structure of an amyloidogenic variant, 3rC34Y, of the germinal line lambda 3 | ||||||
![]() | IG LAMBDA CHAIN V-IV REGION BAU | ||||||
![]() | IMMUNE SYSTEM / AMYLOIDOSIS | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Villalba, M.I. / Luna, O.D. / Rudino-Pinera, E. / Sanchez, R. / Sanchez-Lopez, R. / Rojas-Trejo, S. / Olamendi-Portugal, T. / Fernandez-Velasco, D.A. / Becerril, B. | ||||||
![]() | ![]() Title: Site-Directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human Lambda3R Light Chains. Authors: Villalba, M.I. / Canul-Tec, J.C. / Luna-Martinez, O.D. / Sanchez-Alcala, R. / Olamendi-Portugal, T. / Rudino-Pinera, E. / Rojas, S. / Sanchez-Lopez, R. / Fernandez-Velasco, D.A. / Becerril, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.3 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aizC ![]() 4aj0C ![]() 1lilS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 11403.485 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | BECAUSE THIS VARIANT IS RESULT OF MODIFICATIONS OVER 3RJL2 IT IS NOT DEPOSITED IN ANY DATA BASE. ...BECAUSE THIS VARIANT IS RESULT OF MODIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.96 % / Description: NONE |
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Crystal grow | pH: 3 / Details: 2.3 M AMMONIUM SULFATE, 40 % TREHALOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2011 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.65 Å / Num. obs: 31131 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 16.27 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LIL Resolution: 1.8→24.869 Å / SU ML: 0.48 / σ(F): 2.85 / Phase error: 20.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.558 Å2 / ksol: 0.398 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.869 Å
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Refine LS restraints |
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LS refinement shell |
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