[English] 日本語
Yorodumi- PDB-3wif: Crystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wif | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2beta complex | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / immunogloblin / Anti-Prostaglandin E2 antibody / Prostaglandin E2 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-ON5 Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Sugahara, M. / Ago, H. / Saino, H. / Miyano, M. | ||||||
Citation | Journal: To be Published Title: Crystal structure of anti-Prostaglandin E2 Fab fragment with Prostaglandin E2 Authors: Sugahara, M. / Ago, H. / Saino, H. / Miyano, M. / Kurahashi, Y. / Aoyama, S. / Takehira, M. / Yutani, K. / Yamamoto, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wif.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wif.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/3wif ftp://data.pdbj.org/pub/pdb/validation_reports/wi/3wif | HTTPS FTP |
---|
-Related structure data
Related structure data | 3we6C 3wfhC 3whxC 2ddqS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23511.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma |
---|---|
#2: Antibody | Mass: 23893.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma |
#3: Chemical | ChemComp-ON5 / ( |
#4: Water | ChemComp-HOH / |
Sequence details | THE REFERENCE SEQUENCE OF CHAIN A IS BAL50003 AND CHAIN B IS BAL50004 IN GENBANK. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: oil microbatch / pH: 5 Details: 0.1M Na acetate, 25%(w/v) PEG3350, pH 5.0, OIL MICROBATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2009 |
Radiation | Monochromator: SI(111) DOUBL CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.64 Å / Num. obs: 53235 / % possible obs: 99.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.8 / Num. unique all: 7287 / % possible all: 94.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DDQ Resolution: 1.7→35.33 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8959 / SU ML: 0.18 / σ(F): 1.4 / Phase error: 17.19 / Stereochemistry target values: ML Details: The structure was refined also with REFMAC5 and CNS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.11 Å2 / Biso mean: 20.8515 Å2 / Biso min: 3.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.33 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|