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Yorodumi- PDB-1zea: Structure of the anti-cholera toxin antibody Fab fragment TE33 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zea | ||||||
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Title | Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / polyspecificity / cross-reactivity / anti-cholera toxin / antigen-antibody complex / antigen recognition / substitution matrix | ||||||
Function / homology | Function and homology information IgG immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / immune response / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Scheerer, P. / Krauss, N. / Wessner, H. / Scholz, C. / Otte, L. / Seifert, M. / Kramer, A. / Schneider-Mergener, J. / Hoehne, W. | ||||||
Citation | Journal: J.Mol.Recognit. / Year: 2007 Title: Structure of an anti-cholera toxin antibody Fab in complex with an epitope-derived D-peptide: a case of polyspecific recognition. Authors: Scheerer, P. / Kramer, A. / Otte, L. / Seifert, M. / Wessner, H. / Scholz, C. / Krauss, N. / Schneider-Mergener, J. / Hohne, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zea.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zea.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zea_validation.pdf.gz | 466.9 KB | Display | wwPDB validaton report |
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Full document | 1zea_full_validation.pdf.gz | 474.1 KB | Display | |
Data in XML | 1zea_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 1zea_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/1zea ftp://data.pdbj.org/pub/pdb/validation_reports/ze/1zea | HTTPS FTP |
-Related structure data
Related structure data | 1tetS 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: 23843.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: BALB/c / References: UniProt: A2NHM3 | ||
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#2: Antibody | Mass: 23410.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: BALB/c / References: UniProt: Q921A6 | ||
#3: Protein/peptide | Mass: 990.005 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This D-amino acid sequence occurs peptide synthesis Source: (synth.) synthetic construct (others) | ||
#4: Chemical | #5: 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: 2.33 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 8000, citrat buffer, potassium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8095 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 26, 2001 / Details: bent mirrors |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8095 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→23 Å / Num. all: 40461 / Num. obs: 40461 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.78 % / Biso Wilson estimate: 20.25 Å2 / Rsym value: 0.064 / Net I/σ(I): 14.14 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 3.29 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 1916 / Rsym value: 0.317 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TET Resolution: 1.78→23 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The current model includes the FAB fragment TE33, residues DVA A 1 - DSN A 9 of the bound D-amino acid peptide D2, 276 water molecules and 2 CITRATE ion. The light and heavy chains have been ...Details: The current model includes the FAB fragment TE33, residues DVA A 1 - DSN A 9 of the bound D-amino acid peptide D2, 276 water molecules and 2 CITRATE ion. The light and heavy chains have been designated *L* and *H*, respectively. Peptide has been designated *A*. The numbering of TE33 residues is essentially according to E. KABAT (E.A. KABAT,T.T. WU, H.M. PERRY, K.S. GOTTESMAN, sequences of proteins of Imuunological interest, 5TH ED.,(1991), NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD.). There is no electron density corresponding to the 7-residue stretch H 127 - H 133 in the constant domain of heavy chain H.
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Displacement parameters | Biso mean: 23.0271 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.84 Å / Rfactor Rfree error: 0
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