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Yorodumi- PDB-6wrp: Crystal Structure of PI3-E12 Fab, An Antibody Against Human Parai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wrp | ||||||
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Title | Crystal Structure of PI3-E12 Fab, An Antibody Against Human Parainfluenza Virus Type III | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / FAB | ||||||
Function / homology | AMMONIUM ION / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Weidle, C. / Pancera, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mabs / Year: 2021 Title: Protective antibodies against human parainfluenza virus type 3 infection. Authors: Boonyaratanakornkit, J. / Singh, S. / Weidle, C. / Rodarte, J. / Bakthavatsalam, R. / Perkins, J. / Stewart-Jones, G.B.E. / Kwong, P.D. / McGuire, A.T. / Pancera, M. / Taylor, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wrp.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wrp.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/6wrp ftp://data.pdbj.org/pub/pdb/validation_reports/wr/6wrp | HTTPS FTP |
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-Related structure data
Related structure data | 6mftS 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
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24763.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23772.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Non-polymers , 5 types, 350 molecules
#3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 2.2M Ammonium Sulfate, 2.2% PEG 400, 0.11M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 16, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 24469 / % possible obs: 98 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.41 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.01 |
Reflection shell | Resolution: 2.09→2.13 Å / Num. unique obs: 2026 / CC1/2: 0.905 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MFT Resolution: 2.08→23.79 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.3616 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 30.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→23.79 Å
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Refine LS restraints |
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LS refinement shell |
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