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Yorodumi- PDB-1y18: Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y18 | ||||||
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Title | Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex with hapten | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin / Catalytic antibody / chimeric Fab / Hapten complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HAN Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Debler, E.W. / Ito, S. / Heine, A. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structural origins of efficient proton abstraction from carbon by a catalytic antibody Authors: Debler, E.W. / Ito, S. / Seebeck, F.P. / Heine, A. / Hilvert, D. / Wilson, I.A. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE ...SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE DATABASES. RESIDUE 50 IN CHAINS H,B,D and F WAS MUTATED FROM GLU TO ASP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y18.cif.gz | 342.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y18.ent.gz | 278.9 KB | Display | PDB format |
PDBx/mmJSON format | 1y18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y18_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1y18_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1y18_validation.xml.gz | 68.6 KB | Display | |
Data in CIF | 1y18_validation.cif.gz | 93.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y18 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y18 | HTTPS FTP |
-Related structure data
Related structure data | 1y0lSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23258.826 Da / Num. of mol.: 4 / Mutation: E(H50)D Source method: isolated from a genetically manipulated source Details: The variable domain (residues 1-107) is from a murine source and the constant domain (108-214) is from a human source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 #2: Antibody | Mass: 24572.699 Da / Num. of mol.: 4 / Mutation: E(H50)D Source method: isolated from a genetically manipulated source Details: The variable domain (residues 1-113) is from a murine source and the constant domain (108-233) is from a human source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 #3: Chemical | ChemComp-HAN / #4: Chemical | ChemComp-CL / | #5: 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: 3 Å3/Da / Density % sol: 57 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 Details: Diammonium hydrogen phosphate, NaCl, imidazole HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 110K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2003 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 57674 / Num. obs: 56867 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.089 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2795 / Rsym value: 0.359 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1Y0L Resolution: 2.8→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017
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