+Open data
-Basic information
Entry | Database: PDB / ID: 1hq4 | ||||||
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Title | STRUCTURE OF NATIVE CATALYTIC ANTIBODY HA5-19A4 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CATALYTIC ANTIBODY / TERPENOID SYNTHASE / CARBOCATION / CYCLIZATION CASCADE / IMMUNOGLOBULIN | ||||||
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 / 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. / Lerner, R.A. / Janda, K.D. / Christianson, D.W. | ||||||
Citation | Journal: Thesis / Year: 2000 Title: Polyene Cyclization Reactions Authors: Paschall, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hq4.cif.gz | 172.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hq4.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hq4 ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hq4 | HTTPS FTP |
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-Related structure data
Related structure data | 1cf8S 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.: 2 / Fragment: VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS / 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: Q91W12, UniProt: A0A5E3*PLUS #2: Antibody | Mass: 23442.086 Da / Num. of mol.: 2 / Fragment: VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS / 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 #3: Chemical | #4: 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: 2.51 Å3/Da / Density % sol: 50.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 26, 2000 / 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. all: 25376 / Num. obs: 25376 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 32.001 Å2 / Rsym value: 0.137 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 1.105 % / Mean I/σ(I) obs: 4 / Num. unique all: 2326 / Rsym value: 0.141 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CF8 Resolution: 2.7→20 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood least squares algorithm
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Displacement parameters |
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Refine analyze |
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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→2.72 Å
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Refine LS restraints | *PLUS
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