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- PDB-5vf2: scFv 2D10 re-refined as a complex with trehalose replacing the or... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vf2 | ||||||||||||
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Title | scFv 2D10 re-refined as a complex with trehalose replacing the original alpha-1,6-mannobiose | ||||||||||||
![]() | scFv 2D10 | ||||||||||||
![]() | IMMUNE SYSTEM / IMMUNE SYSTEM RE-REFINEMENT | ||||||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / trehalose![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Porebski, P.J. / Wlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B. | ||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Antibodies Can Exploit Molecular Crowding to Bind New Antigens at Noncanonical Paratope Positions Authors: Vashisht, S. / Kumar, A. / Kaur, K.J. / Salunke, D.M. | ||||||||||||
History |
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Remark 0 | THIS ENTRY 5VF2 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5I4F, DETERMINED BY S. ...THIS ENTRY 5VF2 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5I4F, DETERMINED BY S.VASHISHT,A.KUMAR,K.J.KAUR,D.M.SALUNKE |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.7 KB | Display | ![]() |
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PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5vehC ![]() 5vepC ![]() 5veqC ![]() 5verC ![]() 5vetC ![]() 5vf5C ![]() 5vgaC ![]() 5i4fS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
-Antibody / Sugars , 2 types, 3 molecules A
#1: Antibody | Mass: 26894.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Polysaccharide |
-Non-polymers , 4 types, 323 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MES / | ||||
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#4: Chemical | ChemComp-UNX / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.72 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5I4F |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MES 6.5, Magnesium sulphate (1.5 M), potassium sodium tartrate tetrahydrate (0.1M). |
-Data collection
Diffraction | Mean temperature: 173.15 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.549→50 Å / Num. obs: 41534 / % possible obs: 99.4 % / Redundancy: 5.5 % / Net I/σ(I): 39.67 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I4F Resolution: 1.55→35.11 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.486 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→35.11 Å
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Refine LS restraints |
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