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- PDB-3wif: Crystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wif | ||||||
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Title | Crystal structure of anti-prostaglandin E2 Fab fragment 9Cl-PGF2beta complex | ||||||
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![]() | IMMUNE SYSTEM / immunogloblin / Anti-Prostaglandin E2 antibody / Prostaglandin E2 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-ON5![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugahara, M. / Ago, H. / Saino, H. / Miyano, M. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.7 KB | Display | ![]() |
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PDB format | ![]() | 87.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 689 KB | Display | ![]() |
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Full document | ![]() | 691.2 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3we6C ![]() 3wfhC ![]() 3whxC ![]() 2ddqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: Antibody | Mass: 23893.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: 73.11 Å2 / Biso mean: 20.8515 Å2 / Biso min: 3.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.33 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
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