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Yorodumi- PDB-2h1p: THE THREE-DIMENSIONAL STRUCTURES OF A POLYSACCHARIDE BINDING ANTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h1p | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURES OF A POLYSACCHARIDE BINDING ANTIBODY TO CRYPTOCOCCUS NEOFORMANS AND ITS COMPLEX WITH A PEPTIDE FROM A PHAGE DISPLAY LIBRARY: IMPLICATIONS FOR THE IDENTIFICATION OF PEPTIDE MIMOTOPES | ||||||
Components |
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Keywords | COMPLEX (ANTIBODY/PEPTIDE) / ANTIBODY STRUCTURE / CRYPTOCOCCUS / PHAGE LIBRARY / POLYSACCHARIDE / COMPLEX (ANTIBODY-PEPTIDE) / COMPLEX (ANTIBODY-PEPTIDE) complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Young, A.C.M. / Valadon, P. / Casadevall, A. / Scharff, M.D. / Sacchettini, J.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The three-dimensional structures of a polysaccharide binding antibody to Cryptococcus neoformans and its complex with a peptide from a phage display library: implications for the ...Title: The three-dimensional structures of a polysaccharide binding antibody to Cryptococcus neoformans and its complex with a peptide from a phage display library: implications for the identification of peptide mimotopes. Authors: Young, A.C. / Valadon, P. / Casadevall, A. / Scharff, M.D. / Sacchettini, J.C. #1: Journal: J.Mol.Biol. / Year: 1996 Title: Peptide Libraries Define the Fine Specificity of Anti-Polysaccharide Antibodies to Cryptococcus Neoformans Authors: Valadon, P. / Nussbaum, G. / Boyd, L.F. / Margulies, D.H. / Scharff, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h1p.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h1p.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 2h1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/2h1p ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h1p | HTTPS FTP |
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-Related structure data
Related structure data | 1flrS S: Starting model for refinement |
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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
#1: Antibody | Mass: 24125.727 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source Details: FAB PART ISOLATED AFTER PAPAIN DIGESTION OF THE PARENT IGG1/K MOLECULE Source: (natural) Mus musculus (house mouse) / Cell line: 2H1 BALB/C-NSO HYBRIDOMA / Strain: BALB/C / References: PIR: S16112 |
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#2: Antibody | Mass: 23687.664 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source Details: FAB PART ISOLATED AFTER PAPAIN DIGESTION OF THE PARENT IGG1/K MOLECULE Source: (natural) Mus musculus (house mouse) / Cell line: 2H1 BALB/C-NSO HYBRIDOMA / Strain: BALB/C / References: PIR: S38864 |
#3: Protein/peptide | Mass: 1351.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.2 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: 18% PEG 8K, PH 8.5, 1% GLYCEROL | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: CU K ALPHA / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 19345 / % possible obs: 90 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.4→2.5 Å / % possible all: 79 |
Reflection shell | *PLUS % possible obs: 79 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLR (FAB 4-4-20) Resolution: 2.4→20 Å / Isotropic thermal model: TNT / σ(F): 2 / Stereochemistry target values: TNT
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Solvent computation | Solvent model: TNT | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |