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Yorodumi- PDB-1mfd: THE SOLUTION STRUCTURE OF A TRISACCHARIDE-ANTIBODY COMPLEX: COMPA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mfd | |||||||||
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Title | THE SOLUTION STRUCTURE OF A TRISACCHARIDE-ANTIBODY COMPLEX: COMPARISON OF NMR MEASUREMENTS WITH A CRYSTAL STRUCTURE | |||||||||
Components |
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Keywords | IMMUNOGLOBULIN | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | |||||||||
Authors | Zdanov, A. / Cygler, M. | |||||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Solution structure of a trisaccharide-antibody complex: comparison of NMR measurements with a crystal structure. Authors: Bundle, D.R. / Baumann, H. / Brisson, J.R. / Gagne, S.M. / Zdanov, A. / Cygler, M. #1: Journal: Science / Year: 1991 Title: Recognition of a Cell-Surface Oligo-Saccharide of Pathogenic Salmonella by an Antibody Fab Fragment Authors: Cygler, M. / Rose, D.R. / Bundle, D.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mfd.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mfd.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mfd ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mfd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO L 144 / 2: CIS PROLINE - PRO H 402 / 3: CIS PROLINE - PRO H 404 / 4: CIS PROLINE - PRO H 444 |
-Components
#1: Antibody | Mass: 23125.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 387376 |
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#2: Antibody | Mass: 23570.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 208365 |
#3: Polysaccharide | alpha-D-galactopyranose-(1-2)-[alpha-D-Abequopyranose-(1-3)]methyl alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.96 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging dropDetails: drops were prepared by mixing 0.003 ml of Fab and 0.004 ml of well solution with 0.001 ml of triaccharide | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 24335 / % possible obs: 83 % / Num. measured all: 86916 / Rmerge(I) obs: 0.047 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.183 / Rfactor obs: 0.183 / Highest resolution: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(I): 2 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.1 |