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Yorodumi- PDB-3trs: The crystal structure of aspergilloglutamic peptidase from Asperg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3trs | ||||||
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Title | The crystal structure of aspergilloglutamic peptidase from Aspergillus niger | ||||||
Components |
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Keywords | HYDROLASE / ASPERGILLOGLUTAMIC PEPTIDASE / GLUTAMIC PEPTIDASE / 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 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sasaki, H. / Kubota, K. / Lee, W.C. / Ohtsuka, J. / Kojima, M. / Takahashi, K. / Tanokura, M. | ||||||
Citation | Journal: J.Biochem. / Year: 2012 Title: The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis. Authors: Sasaki, H. / Kubota, K. / Lee, W.C. / Ohtsuka, J. / Kojima, M. / Iwata, S. / Nakagawa, A. / 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 | 3trs.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3trs.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 3trs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/3trs ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3trs | HTTPS FTP |
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-Related structure data
Related structure data | 1y43S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3919.114 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Strain: Var. macrosporus / References: UniProt: P24665, aspergillopepsin II #2: Protein | Mass: 18372.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Strain: Var. macrosporus / References: UniProt: P24665, aspergillopepsin II #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 2.7 Details: 1.3M AMMONIUM SULFATE, 0.1M GLYCINE BUFFER (PH 2.7), 5% (V/V) DMSO, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 37983 / % possible obs: 95.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.25 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.24 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y43 Resolution: 1.6→38.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.296 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→38.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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