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- PDB-1f4y: CRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f4y | |||||||||
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Title | CRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAINST VIBRIO CHOLERAE O1 IN COMPLEX WITH ANTIGEN | |||||||||
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![]() | IMMUNE SYSTEM / anti-carbohydrate antibody | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Alzari, P.M. / Souchon, H. | |||||||||
![]() | ![]() Title: Crystal structure of an anti-carbohydrate antibody directed against Vibrio cholerae O1 in complex with antigen: molecular basis for serotype specificity. Authors: Villeneuve, S. / Souchon, H. / Riottot, M.M. / Mazie, J.C. / Lei, P. / Glaudemans, C.P. / Kovac, P. / Fournier, J.M. / Alzari, P.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.6 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.9 KB | Display | ![]() |
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Full document | ![]() | 510.9 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 22527.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23274.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Polysaccharide | 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranose-(1-2)-methyl 4,6- ...4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranose-(1-2)-methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source |
Sequence details | THE ATOMIC COORDINATES IN THIS ENTRY FOLLOW A CORRELATIVE NUMBERING SCHEME. INSTEAD, KABAT ...THE ATOMIC COORDINATE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.25 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 6000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.2 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 9638 / Num. obs: 9638 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.296 / % possible all: 91.3 |
Reflection | *PLUS Num. measured all: 27225 |
Reflection shell | *PLUS % possible obs: 91.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: STRUCTURE OF THE UNLIGANDED FAB FRAGMENT Resolution: 2.8→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.507 / Rfactor Rwork: 0.272 |