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Yorodumi- PDB-1cf8: Convergence of catalytic antibody and terpene cyclase mechanisms:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cf8 | ||||||
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Title | Convergence of catalytic antibody and terpene cyclase mechanisms: polyene cyclization directed by carbocation-pi interactions | ||||||
Components |
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Keywords | CATALYTIC ANTIBODY / TERPENOID SYNTHASE / CARBOCATION / CYCLIZATION CASCADE | ||||||
Function / homology | Function and homology information Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Paschall, C.M. / Hasserodt, J. / Jones, T. / Lerner, R.A. / Janda, K.D. / Christianson, D.W. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 1999 Title: Convergence of Catalytic Antibody and Terpene Cyclase Mechanisms: Polyene Cyclization Directed by Carbocation-pi Interactions Authors: Paschall, C.M. / Hasserodt, J. / Jones, T. / Lerner, R.A. / Janda, K.D. / Christianson, D.W. | ||||||
History |
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Remark 999 | SEQUENCE The proper sequence database reference not availabe due to fragments of variable region |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cf8.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cf8.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 1cf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/1cf8 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/1cf8 | HTTPS FTP |
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-Related structure data
Related structure data | 1yefS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23484.854 Da / Num. of mol.: 1 / Fragment: FAB, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 129G1X+(MOUSE)/P3X63AG8.653 (MYELOMA) / Strain: 129G1X+/BOY / References: UniProt: P01837*PLUS | ||||||
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#2: Antibody | Mass: 23500.123 Da / Num. of mol.: 1 / Fragment: FAB, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 129G1X+(MOUSE)/P3X63AG8.653 (MYELOMA) / Strain: 129G1X+/BOY / References: UniProt: P01867*PLUS | ||||||
#3: Chemical | #4: Chemical | ChemComp-HAZ / | #5: Water | ChemComp-HOH / | Compound details | THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ...THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 47.8 % Description: USED MODEL OF SEQUENCE WITH ONLY VARYING RESIDUES CHANGED TO ALANINE. | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: DROP: 11.4 MG/ML FAB, 10MM CDCL2, 50 MM TRIS, PH 7.0, RESERVOIR: 30% PEG 6000, 100 MM HEPES PH 7.9, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 17, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 11531 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.31 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 6.7 / % possible all: 80.2 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Biso Wilson estimate: 39.1 Å2 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 6.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YEF Resolution: 2.7→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor obs: 0.165 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.299 / Rfactor Rwork: 0.232 |