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- PDB-5l88: AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l88 | |||||||||
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Title | AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM I, non-parsimonious model | |||||||||
![]() | (Anti-afamin antibody N14, Fab fragment, ...) x 2 | |||||||||
![]() | IMMUNE SYSTEM / Afamin antibody / Fab Fragment / IgG1-kappa / light chain glycosilation | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rupp, B. / Naschberger, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling. Authors: Naschberger, A. / Furnrohr, B.G. / Lenac Rovis, T. / Malic, S. / Scheffzek, K. / Dieplinger, H. / Rupp, 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 | ![]() | 193 KB | Display | ![]() |
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PDB format | ![]() | 151.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 951.9 KB | Display | ![]() |
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Full document | ![]() | 958.2 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l7xC ![]() 5l9dC ![]() 5lghC ![]() 1il1S 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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Unit cell |
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Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23686.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23658.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 7 types, 267 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/PE8.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PE8.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PG4 / #5: Chemical | ChemComp-PE8 / | #6: Chemical | ChemComp-PGE / #7: Chemical | #8: Chemical | ChemComp-K / | #9: Chemical | ChemComp-1PE / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.9 % Description: Block-shaped crystals with sharp edges (0.15 x 0.15 x 0.3 mm) |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.8 Details: 200nL Fab 10mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl plus 200nL 30%w/v PEG 1k, 200mM KF, pH 5.8) Temp details: Air conditioned room |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015 / Details: Torroidal focussing mirror |
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: 1.88→54.37 Å / Num. obs: 34249 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IL1 Resolution: 1.88→47.38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.297 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.307 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→47.38 Å
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Refine LS restraints |
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