[English] 日本語
Yorodumi- PDB-1a0q: 29G11 COMPLEXED WITH PHENYL [1-(1-N-SUCCINYLAMINO)PENTYL] PHOSPHONATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a0q | ||||||
---|---|---|---|---|---|---|---|
Title | 29G11 COMPLEXED WITH PHENYL [1-(1-N-SUCCINYLAMINO)PENTYL] PHOSPHONATE | ||||||
Components |
| ||||||
Keywords | CATALYTIC ANTIBODY / ESTERASE | ||||||
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 / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Buchbinder, J.L. / Stephenson, R.C. / Scanlan, T.S. / Fletterick, R.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: A comparison of the crystallographic structures of two catalytic antibodies with esterase activity. Authors: Buchbinder, J.L. / Stephenson, R.C. / Scanlan, T.S. / Fletterick, R.J. #1: Journal: Science / Year: 1994 Title: Crystal Structure of a Catalytic Antibody with a Serine Protease Active Site Authors: Zhou, G.W. / Guo, J. / Huang, W. / Fletterick, R.J. / Scanlan, T.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a0q.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a0q.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 1a0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a0q_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1a0q_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 1a0q_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1a0q_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0q ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0q | HTTPS FTP |
-Related structure data
Related structure data | 1eapS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23641.271 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source Details: PHENYL [1-(1-N-SUCCINYLAMINO)PENTYL]PHOSPHONATE HAPTEN Source: (natural) Mus musculus (house mouse) / References: GenBank: 12002896, UniProt: P01837*PLUS | ||||
---|---|---|---|---|---|
#2: Antibody | Mass: 23343.070 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source Details: PHENYL [1-(1-N-SUCCINYLAMINO)PENTYL]PHOSPHONATE HAPTEN Source: (natural) Mus musculus (house mouse) / References: GenBank: 3399661, UniProt: P01869*PLUS | ||||
#3: Chemical | #4: Chemical | ChemComp-HEP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 42.48 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 20072 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.089 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.3 / % possible all: 90.2 |
Reflection | *PLUS Num. measured all: 85418 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDP ENTRY 1EAP Resolution: 2.3→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|