+Open data
-Basic information
Entry | Database: PDB / ID: 3t77 | ||||||||||||
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Title | S25-2- A(2-4)KDO disaccharide complex | ||||||||||||
Components | (S25-2 FAB (IGG1K) ...) x 2 | ||||||||||||
Keywords | IMMUNE SYSTEM / antigen-binding fragment / FAB / anti-carbohydrate / anti-LPS / antibody / immunoglobulin / KDO | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.739 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 | 3t77.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t77.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 3t77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t77_validation.pdf.gz | 838.5 KB | Display | wwPDB validaton report |
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Full document | 3t77_full_validation.pdf.gz | 848.9 KB | Display | |
Data in XML | 3t77_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3t77_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/3t77 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/3t77 | HTTPS FTP |
-Related structure data
Related structure data | 1q9kC 1q9lC 1q9oC 1q9wC 3sy0C 3t4yC 3t65C 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) / References: UniProt: Q52L64*PLUS |
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#2: Antibody | Mass: 24329.199 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
#3: Polysaccharide | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid Type: oligosaccharide / Mass: 498.433 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 409 molecules
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: KDO disaccharide, magnesium chloride, zinc chloride, ethylene glycol, glycerol, PEG 4000, TRIS, pH 8.0, VAPOR DIFFUSION, 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: Jun 21, 2002 / 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: 1.74→19.82 Å / Num. obs: 47589 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.739→19.823 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8212 / SU ML: 0.44 / σ(F): 1 / Phase error: 24.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.933 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.97 Å2 / Biso mean: 32.2384 Å2 / Biso min: 15.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.739→19.823 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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