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- PDB-6srx: Structure of the arginase-2-inhibitory human antigen-binding frag... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6srx | ||||||
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Title | Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021158 | ||||||
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![]() | PROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment | ||||||
Function / homology | ACETATE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Burschowsky, D. / Addyman, A. / Fiedler, S. / Groves, M. / Haynes, S. / Seewooruthun, C. / Carr, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional characterization of C0021158, a high-affinity monoclonal antibody that inhibits Arginase 2 function via a novel non-competitive mechanism of action. Authors: Austin, M. / Burschowsky, D. / Chan, D.T.Y. / Jenkinson, L. / Haynes, S. / Diamandakis, A. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / ...Authors: Austin, M. / Burschowsky, D. / Chan, D.T.Y. / Jenkinson, L. / Haynes, S. / Diamandakis, A. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / Hadjinicolaou, A.V. / Gileadi, U. / Gowans, E. / Shibata, Y. / Barnard, M. / Kaserer, T. / Sharma, P. / Luheshi, N.M. / Wilkinson, R.W. / Vaughan, T.J. / Holt, S.V. / Cerundolo, V. / Carr, M.D. / Groves, M.A.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 576.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.3 KB | Display | ![]() |
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Full document | ![]() | 476.8 KB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 47.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6srvSC ![]() 6ss0C ![]() 6ss2C ![]() 6ss4C ![]() 6tulC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Antibody | Mass: 24647.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Amino acids are numbered according to the Kabat numbering scheme. Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): ExpiCHO #2: Antibody | Mass: 23137.520 Da / Num. of mol.: 2 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.) ![]() Production host: ![]() ![]() Strain (production host): ExpiCHO #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM NaAcO pH 5.0 20% PEG6000 200 mM LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.96 Å / Num. obs: 67778 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4374 / CC1/2: 0.53 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SRV Resolution: 1.9→48.955 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.373 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.193 / ESU R Free: 0.164 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.864 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.955 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: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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