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Yorodumi- PDB-3wfh: Crystal structure of anti-Prostaglandin E2 Fab fragment PGE2 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wfh | ||||||
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Title | Crystal structure of anti-Prostaglandin E2 Fab fragment PGE2 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunogloblin / Anti-Prostaglandin E2 antibody / prostaglandin E2 / Fab fragment by papain digestion | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-P2E Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wfh.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wfh.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/3wfh ftp://data.pdbj.org/pub/pdb/validation_reports/wf/3wfh | HTTPS FTP |
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-Related structure data
Related structure data | 3we6C 3whxC 3wifC 2ddqS 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
#1: Antibody | Mass: 23396.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma |
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#2: Antibody | Mass: 23779.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma |
#3: Chemical | ChemComp-P2E / ( |
#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 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 293 K / Method: oil microbatch / pH: 6 Details: 30%(w/v) PEG 4000, 0.2M ammonium sulfate, 0.1M Na-citrate, pH 6.0, OIL MICROBATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 1.9→35.13 Å / Num. obs: 38574 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.138 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.4 / Num. unique all: 5547 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DDQ Resolution: 1.9→35.13 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8948 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 17.26 / Stereochemistry target values: ML / Details: The structure was refined also REFMAC5 and CNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.97 Å2 / Biso mean: 22.1638 Å2 / Biso min: 3.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→35.13 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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