[English] 日本語
Yorodumi- PDB-6zvf: Crystal structure of the recombinant Fab fragment derived from th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zvf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the recombinant Fab fragment derived from the hybridoma M3/38 in complex with a human Galectin-3 peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / ANTIBODY / FAB FRAGMENT / PEPTIDE EPITOPE / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / macrophage chemotaxis / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Skerra, A. / Eichinger, A. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2021 Title: Effective rational humanization of a PASylated anti-galectin-3 Fab for the sensitive PET imaging of thyroid cancer in vivo. Authors: Peplau, E. / De Rose, F. / Eichinger, A. / Reder, S. / Mittelhauser, M. / Scafetta, G. / Schwaiger, M. / Weber, W.A. / Bartolazzi, A. / D'Alessandria, C. / Skerra, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zvf.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zvf.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/6zvf ftp://data.pdbj.org/pub/pdb/validation_reports/zv/6zvf | HTTPS FTP |
---|
-Related structure data
Related structure data | 3o2vS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23927.803 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Both immunoglobulin chains (L, H) are linked by a disulfide bond (CYS219L to CYS221H). Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) |
---|---|
#2: Antibody | Mass: 24392.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 222 - 227 represent an affinity tag (His6-tag). Both immunoglobulin chains (L, H) are linked by a disulfide bond (CYS219L to CYS221H). Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) |
#3: Protein/peptide | Mass: 882.959 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide QAPPGAYPG carries an acetyl (ACE) group at the N-terminus. Source: (synth.) Homo sapiens (human) / References: UniProt: P17931 |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2018 / Details: Si mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.661→78.719 Å / Num. all: 34354 / Num. obs: 34354 / % possible obs: 97 % / Redundancy: 5.7 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Rsym value: 0.088 / Net I/av σ(I): 5.7 / Net I/σ(I): 10.9 / Num. measured all: 197033 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O2V Resolution: 1.9→50.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.385 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 88.63 Å2 / Biso mean: 25.385 Å2 / Biso min: 12.98 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→50.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|