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Yorodumi- PDB-1riv: Anti-Cocaine Antibody M82G2 Complexed With meta-Oxybenzoylecgonine -
+Open data
-Basic information
Entry | Database: PDB / ID: 1riv | ||||||
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Title | Anti-Cocaine Antibody M82G2 Complexed With meta-Oxybenzoylecgonine | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTI-COCAINE ANTIBODY / FAB | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-OBE Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pozharski, E. / Hewagama, A. / Shanafelt, A. / Petsko, G. / Ringe, D. | ||||||
Citation | Journal: To be Published Title: Carving a Binding Site: Structural Study of an Anti-Cocaine Antibody in Complex with Three Cocaine Analogs Authors: Pozharski, E. / Hewagama, A. / Shanafelt, A. / Petsko, G. / Ringe, D. | ||||||
History |
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Remark 999 | SEQUENCE A suitable database reference sequence could not be found for chains L and H at the time ...SEQUENCE A suitable database reference sequence could not be found for chains L and H at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1riv.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1riv.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 1riv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1riv ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1riv | HTTPS FTP |
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-Related structure data
Related structure data | 1riuC 1ar3 1axtS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 23884.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23519.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Chemical | ChemComp-OBE / |
#4: 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: 2.57 Å3/Da / Density % sol: 51.7 % Description: CRYSTALS WERE TRANSFERRED STEPWISE INTO 70% SATURATED SODIUM MALONATE, PH 7.2, AND SUBSEQUENTLY SOAKED OVERNIGHT IN THE SODIUM MALONATE SOLUTION CONTAINING 300 MICROMOLAR OXYBENZOYLECGONINE-HCL |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 2M AMMONIUM SULFATE, 5% ISO-PROPANOL, pH 5.20, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2002 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→38 Å / Num. all: 26936 / Num. obs: 26936 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 43.8 Å2 / Rsym value: 0.119 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.62 % / Mean I/σ(I) obs: 1.97 / Num. unique all: 2637 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AR3 (CONSTANT DOMAIN) + PDB ENTRY 1AXT (VARIABLE DOMAIN) Resolution: 2.2→38 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: BULK SOLVENT MASK CORRECTED TO EXCLUDE INTERNAL CAVITIES
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Solvent computation | Solvent model: MASK / Bsol: 48.9 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Total num. of bins used: 10
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