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Yorodumi- PDB-6ss6: Structure of arginase-2 in complex with the inhibitory human anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ss6 | ||||||
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Title | Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0020187 | ||||||
Components |
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Keywords | PROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment | ||||||
Function / homology | Function and homology information negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginase ...negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-17 production / regulation of reactive oxygen species biosynthetic process / ureteric bud development / negative regulation of tumor necrosis factor production / Mitochondrial protein degradation / striated muscle contraction / nitric oxide biosynthetic process / positive regulation of cellular senescence / manganese ion binding / adaptive immune response / mitochondrial matrix / innate immune response / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Burschowsky, D. / Addyman, A. / Fiedler, S. / Groves, M. / Haynes, S. / Seewooruthun, C. / Carr, M. | ||||||
Funding support | United Kingdom, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ss6.cif.gz | 821.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ss6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ss6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/6ss6 ftp://data.pdbj.org/pub/pdb/validation_reports/ss/6ss6 | HTTPS FTP |
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-Related structure data
Related structure data | 6ss5SC 4hzeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 37808.594 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78540, arginase #2: Antibody | Mass: 24479.453 Da / Num. of mol.: 3 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: Cricetulus griseus (Chinese hamster) / Variant (production host): ExpiCHO #3: Antibody | Mass: 23064.469 Da / Num. of mol.: 3 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 #4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-SO4 / 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: 2.96 Å3/Da / Density % sol: 58.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→48.78 Å / Num. obs: 50453 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.78 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 3.25→3.36 Å / Redundancy: 9.9 % / Rmerge(I) obs: 8.48 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4555 / CC1/2: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HZE,6SS5 Resolution: 3.25→48.755 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.825 / SU B: 66.427 / SU ML: 0.949 / Cross valid method: FREE R-VALUE / ESU R Free: 0.711 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: 99.097 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→48.755 Å
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Refine LS restraints |
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