+Open data
-Basic information
Entry | Database: PDB / ID: 7y0g | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-mPEG h15-2b Fab | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / methoxy polyethylene glycol / anti-mPEG antibody | |||||||||
Function / homology | 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | |||||||||
Authors | Chang, C.Y. / Nguyen, T.M.T. / Lin, E.C. / Su, Y.C. | |||||||||
Funding support | Taiwan, 2items
| |||||||||
Citation | Journal: Commun Chem / Year: 2022 Title: Structural determination of an antibody that specifically recognizes polyethylene glycol with a terminal methoxy group. Authors: Nguyen, M.T. / Shih, Y.C. / Lin, M.H. / Roffler, S.R. / Hsiao, C.Y. / Cheng, T.L. / Lin, W.W. / Lin, E.C. / Jong, Y.J. / Chang, C.Y. / Su, Y.C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7y0g.cif.gz | 339.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7y0g.ent.gz | 275.5 KB | Display | PDB format |
PDBx/mmJSON format | 7y0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y0g_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7y0g_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7y0g_validation.xml.gz | 64.3 KB | Display | |
Data in CIF | 7y0g_validation.cif.gz | 91.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/7y0g ftp://data.pdbj.org/pub/pdb/validation_reports/y0/7y0g | HTTPS FTP |
-Related structure data
Related structure data | 1l7iS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23539.170 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 24598.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Chemical | ChemComp-P15 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% (w/v) PEG-6000, 1% (w/v) PEG-2000-MME, 0.15 M lithium sulfate monohydrate, and 0.1 M citric acid |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9732 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9732 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→30 Å / Num. obs: 131932 / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.77 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 12417 / CC1/2: 0.864 / CC star: 0.963 / % possible all: 93.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L7I Resolution: 2.08→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.877 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.08 Å2 / Biso mean: 28.829 Å2 / Biso min: 12.06 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.084→2.138 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|