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Yorodumi- PDB-3whx: Crystal structure of anti-prostaglandin E2 Fab fragment PGE1 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3whx | ||||||
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Title | Crystal structure of anti-prostaglandin E2 Fab fragment PGE1 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunogloblin / Anti-Prostaglandin E2 antibody / Prostaglandin E2 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-XPG 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3whx.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3whx.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 3whx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/3whx ftp://data.pdbj.org/pub/pdb/validation_reports/wh/3whx | HTTPS FTP |
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-Related structure data
Related structure data | 3we6C 3wfhC 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: 23511.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma |
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#2: Antibody | Mass: 23893.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma |
#3: Chemical | ChemComp-XPG / |
#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: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 293 K / Method: oil-microbatch / pH: 6 Details: 0.1M bis-tris-HCl, 25%(w/v) PEG3350 , 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: 1.7→29.05 Å / Num. obs: 53198 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 4.7 / Num. unique all: 7665 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DDQ Resolution: 1.7→26.763 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.895 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 17.27 / 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: 68.08 Å2 / Biso mean: 19.3299 Å2 / Biso min: 2.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→26.763 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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