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Open data
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Basic information
Entry | Database: PDB / ID: 3t4y | |||||||||
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Title | S25-2- KDO monosaccharide complex | |||||||||
![]() | (S25-2 FAB (IGG1K) ...) x 2 | |||||||||
![]() | IMMUNE SYSTEM / ANTIGEN-BINDING FRAGMENT / FAB / ANTI-CARBOHYDRATE / ANTI-LPS / ANTIBODY / IMMUNOGLOBULIN / KDO | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nguyen, H.P. / Seto, N.O. / Mackenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V. | |||||||||
![]() | ![]() Title: Germline antibody recognition of distinct carbohydrate epitopes. Authors: Nguyen, H.P. / Seto, N.O. / MacKenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.2 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 459.3 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 37.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q9kC ![]() 1q9lC ![]() 1q9oC ![]() 1q9wC ![]() 3sy0C ![]() 3t65C ![]() 3t77C ![]() 1q9r 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
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 24242.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 24110.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/KDO.gif)
#4: Sugar | ChemComp-KDO / |
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-Non-polymers , 3 types, 572 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-ZN / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 293 K / Method: hanging drop / pH: 8 Details: KDO MONOSACCHARIDE, MAGNESIUM CHLORIDE, ZINC CHLORIDE, ETHYLENE GLYCOL, GLYCEROL, PEG 4000, TRIS, pH 8.0, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003 / Details: mirrors |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→19.97 Å / Num. obs: 43168 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Q9R ![]() 1q9r Resolution: 1.73→19.452 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8652 / SU ML: 0.47 / σ(F): 1 / Phase error: 20.64 / 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: 33.371 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.77 Å2 / Biso mean: 20.9531 Å2 / Biso min: 6.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→19.452 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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