[English] 日本語
Yorodumi- PDB-6ss5: Structure of the arginase-2-inhibitory human antigen-binding frag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ss5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0020187 | ||||||
Components | (Fab C0020187 ...) x 2 | ||||||
Keywords | PROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Burschowsky, D. / Addyman, A. / Fiedler, S. / Groves, M. / Haynes, S. / Seewooruthun, C. / Carr, M. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Extensive sequence and structural evolution of Arginase 2 inhibitory antibodies enabled by an unbiased approach to affinity maturation. Authors: Chan, D.T.Y. / Jenkinson, L. / Haynes, S.W. / Austin, M. / Diamandakis, A. / Burschowsky, D. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / ...Authors: Chan, D.T.Y. / Jenkinson, L. / Haynes, S.W. / Austin, M. / Diamandakis, A. / Burschowsky, D. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / Gowans, E. / Shibata, Y. / Barnard, M. / Wilkinson, R.W. / Vaughan, T.J. / Holt, S.V. / Cerundolo, V. / Carr, M.D. / Groves, M.A.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ss5.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ss5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ss5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/6ss5 ftp://data.pdbj.org/pub/pdb/validation_reports/ss/6ss5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ss6C 6srvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Antibody , 2 types, 2 molecules HHHLLL
#1: Antibody | Mass: 24479.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Amino acids are numbered according to the Kabat numbering scheme. Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU1.3 fab / Cell line (production host): CHO Production host: Cricetinae gen. sp.Cricetulus griseus (Chinese hamster) Variant (production host): ExpiCHO |
---|---|
#2: Antibody | Mass: 23064.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Amino acids are numbered according to the Kabat numbering scheme. Residue 10 would not be present in the Kabat scheme, but due to problems with non-continuous numbering in L-peptides, we ...Details: Amino acids are numbered according to the Kabat numbering scheme. Residue 10 would not be present in the Kabat scheme, but due to problems with non-continuous numbering in L-peptides, we included it. Therefore, residues 2-10 should be read as 1-9, per Kabat. Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU1.3 fab / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): ExpiCHO |
-Non-polymers , 5 types, 329 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→49.355 Å / Num. obs: 58306 / % possible obs: 99.7 % / Redundancy: 10.4 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.78→1.82 Å / Redundancy: 8.5 % / Rmerge(I) obs: 4.11 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3268 / CC1/2: 0.31 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SRV Resolution: 1.78→49.354 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.725 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.102 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.211 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→49.354 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|