+Open data
-Basic information
Entry | Database: PDB / ID: 3t4y | |||||||||
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Title | S25-2- KDO monosaccharide complex | |||||||||
Components | (S25-2 FAB (IGG1K) ...) x 2 | |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | |||||||||
Authors | Nguyen, H.P. / Seto, N.O. / Mackenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t4y.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t4y.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 3t4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t4y_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 3t4y_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 3t4y_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 3t4y_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4y ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4y | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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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.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
-Sugars , 1 types, 1 molecules
#4: Sugar | ChemComp-KDO / |
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-Non-polymers , 3 types, 572 molecules
#3: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-ZN / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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