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Yorodumi- PDB-6s1y: Crystal structure of Anopheles gambiae AnoACE2 in complex with ga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s1y | |||||||||
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Title | Crystal structure of Anopheles gambiae AnoACE2 in complex with gamma-Polyglutamic Acid. | |||||||||
Components | Angiotensin-converting enzyme | |||||||||
Keywords | HYDROLASE / metalloprotease / mosquito control / insecticide design | |||||||||
Function / homology | Function and homology information metallodipeptidase activity / Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / proteolysis / extracellular space / zinc ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Anopheles gambiae (African malaria mosquito) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Cozier, G.E. / Acharya, K.R. / Cashman, J.S. | |||||||||
Citation | Journal: Biochem.J. / Year: 2019 Title: Crystal structures of angiotensin-converting enzyme from Anopheles gambiae in its native form and with a bound inhibitor. Authors: Cashman, J.S. / Cozier, G.E. / Harrison, C. / Isaac, R.E. / Acharya, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s1y.cif.gz | 248.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s1y.ent.gz | 200.4 KB | Display | PDB format |
PDBx/mmJSON format | 6s1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s1y_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6s1y_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6s1y_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 6s1y_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s1y ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s1y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 72041.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: ANCE2, AgaP_AGAP009751 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: A0NFU8, Hydrolases; Acting on peptide bonds (peptidases) |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 203 molecules
#4: Chemical | ChemComp-PEG / | ||||||
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#5: Chemical | #6: Chemical | ChemComp-ZN / | #7: Chemical | ChemComp-KSN / ( | #8: Water | ChemComp-HOH / | |
-Details
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: 3.16 Å3/Da / Density % sol: 61.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 36% v/v polypropylene glycol, 30 mM sodium formate, 10 mM Tris pH 7.8, 0.3 % w/v gamma-PGA, 0.3% w/v PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→139.41 Å / Num. obs: 47663 / % possible obs: 100 % / Redundancy: 38.2 % / CC1/2: 0.998 / Rpim(I) all: 0.052 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 39.2 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4072 / CC1/2: 0.551 / Rpim(I) all: 1.121 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AnoACE2 homology model Resolution: 2.2→91.76 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→91.76 Å
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Refine LS restraints |
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LS refinement shell |
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