+Open data
-Basic information
Entry | Database: PDB / ID: 7wa3 | ||||||
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Title | Structure of American mink ACE2 | ||||||
Components | Angiotensin-converting enzyme | ||||||
Keywords | HYDROLASE / SARS-CoV-2 spike receptor-binding domain | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / apical plasma membrane / proteolysis / extracellular region / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Neovison vison (American mink) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Su, C. / Qi, J.X. / Gao, G.F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The molecular basis of SARS-CoV-2 variants binding to mink ACE2 Authors: Su, C. / He, J.H. / Qi, J.X. / Yang, M.S. / Wang, Q.H. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wa3.cif.gz | 570.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wa3.ent.gz | 416.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wa3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/7wa3 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/7wa3 | HTTPS FTP |
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-Related structure data
Related structure data | 1r42S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 70562.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neovison vison (American mink) / Production host: Trichoplusia ni (cabbage looper) References: UniProt: A0A7T0Q2W2, Hydrolases; Acting on peptide bonds (peptidases) #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Potassium thiocyanate, 30% w/v PEG 2000 MME2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→71.54 Å / Num. obs: 61639 / % possible obs: 98.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 32.7 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.142 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.28→2.4 Å / Rmerge(I) obs: 0.591 / Num. unique obs: 9035 / CC1/2: 0.737 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R42 Resolution: 2.28→42.19 Å / SU ML: 0.3011 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4335 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→42.19 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.96243616926 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 19 - 800 / Label seq-ID: 1
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