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Yorodumi- PDB-1y43: crystal structure of aspergilloglutamic peptidase from Aspergillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y43 | ||||||
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Title | crystal structure of aspergilloglutamic peptidase from Aspergillus niger | ||||||
Components |
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Keywords | HYDROLASE / aspergillopepsin II / proctase A / beta sandwich structure | ||||||
Function / homology | Function and homology information aspergillopepsin II / glutamic-type endopeptidase activity / aspartic-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Aspergillus niger var. macrosporus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.4 Å | ||||||
Authors | Sasaki, H. / Nakagawa, A. / Iwata, S. / Muramatsu, T. / Suganuma, M. / Sawano, Y. / Kojima, M. / Kubota, K. / Takahashi, K. | ||||||
Citation | Journal: Proc.Jpn.Acad.,Ser.B / Year: 2004 Title: The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger Authors: Sasaki, H. / Nakagawa, A. / Muramatsu, T. / Suganuma, M. / Sawano, Y. / Kojima, M. / Kubota, K. / Takahashi, K. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y43.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y43.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 1y43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y43_validation.pdf.gz | 376.1 KB | Display | wwPDB validaton report |
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Full document | 1y43_full_validation.pdf.gz | 376 KB | Display | |
Data in XML | 1y43_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1y43_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/1y43 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/1y43 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3919.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger var. macrosporus (mold) / Species: Aspergillus niger / Strain: Var. Macrosporus / References: UniProt: P24665, aspergillopepsin II | ||
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#2: Protein | Mass: 18372.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger var. macrosporus (mold) / Species: Aspergillus niger / Strain: Var. Macrosporus / References: UniProt: P24665, aspergillopepsin II | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 2.1 Details: ammonium sulfate, dimethyl sulfoxide, glycine, pH 2.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 30, 1993 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. obs: 29424 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.4→1.44 Å / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.4→10 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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LS refinement shell | Resolution: 1.4→1.46 Å
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