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Yorodumi- PDB-1axt: IMMUNE VERSUS NATURAL SELECTION: ANTIBODY ALDOLASES WITH THE RATE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1axt | ||||||
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Title | IMMUNE VERSUS NATURAL SELECTION: ANTIBODY ALDOLASES WITH THE RATES OF NATURAL ENZYMES | ||||||
Components | (IMMUNOGLOBULIN IGG2A) x 2 | ||||||
Keywords | IMMUNOGLOBULIN / ANTIBODY FAB' / CATALYST / ALDOLASE REACTION | ||||||
Function / homology | Function and homology information positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Heine, A. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 1997 Title: Immune versus natural selection: antibody aldolases with enzymic rates but broader scope. Authors: Barbas 3rd., C.F. / Heine, A. / Zhong, G. / Hoffmann, T. / Gramatikova, S. / Bjornestedt, R. / List, B. / Anderson, J. / Stura, E.A. / Wilson, I.A. / Lerner, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1axt.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1axt.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 1axt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1axt ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1axt | HTTPS FTP |
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-Related structure data
Related structure data | 2cgrS 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: 23796.426 Da / Num. of mol.: 1 / Fragment: FAB' FRAGMENT 33F12 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY IGG2A FAB' FRAGMENT / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: PIR: S16112 |
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#2: Antibody | Mass: 23829.885 Da / Num. of mol.: 1 / Fragment: FAB' FRAGMENT 33F12 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY IGG2A FAB' FRAGMENT / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01865 |
#3: 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: 2.45 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.4. | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: PT COATED FUSED SILICA X-RAY MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 26432 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.065 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.302 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 264288 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.302 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CGR Resolution: 2.15→10 Å / Num. parameters: 14365 / Num. restraintsaints: 14062 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THE INITIAL REFINEMENT WAS BEGUN USING X-PLOR. RESIDUES H 128 TO H136 ARE IN WEAK OR NO ELECTRON DENSITY. THEY WERE REFINED WITH ZERO OCCUPANCY AND THE LISTED COORDINATES ARE THEREFORE NOT RELIABLE.
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 3233 / Occupancy sum non hydrogen: 3556 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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