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Yorodumi- PDB-1j71: Structure of the extracellular aspartic proteinase from Candida t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j71 | ||||||
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Title | Structure of the extracellular aspartic proteinase from Candida tropicalis yeast. | ||||||
Components |
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Keywords | HYDROLASE / Candida tropicalis aspartic protease / SAPT1 | ||||||
Function / homology | Function and homology information candidapepsin / aspartic-type endopeptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Candida tropicalis (yeast) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Symersky, J. / Monod, M. / Foundling, S.I. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: High-resolution structure of the extracellular aspartic proteinase from Candida tropicalis yeast. Authors: Symersky, J. / Monod, M. / Foundling, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j71.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j71.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j71 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j71 | HTTPS FTP |
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-Related structure data
Related structure data | 1zapS 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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Unit cell |
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-Components
#1: Protein | Mass: 35954.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida tropicalis (yeast) / References: UniProt: Q00663, candidapepsin | ||
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#2: Protein/peptide | Mass: 420.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified (others) | ||
#3: Chemical | ChemComp-EOH / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: VAPOR DIFFUSION BY HANGING DROPS. 0.1 M SODIUM ACETATE, 20% ETHANOL, 1:1 WITH WATER SOLUTION OF THE PROTEIN (30 MG/ML)., pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jun 27, 1994 / Details: monochromator |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 110551 / Num. obs: 99496 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.36 / Redundancy: 3.5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 19 |
Reflection | *PLUS Num. obs: 32636 / Num. measured all: 215435 / Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZAP Resolution: 1.8→27.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 60546.12 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 2 / σ(I): 1.36 / Stereochemistry target values: Engh & Huber Details: A TETRAPEPTIDE OF UNKNOWN SOURCE FOUND AT THE ACTIVE SITE REFINED BEST AS THR-ILE-THR-SER. HOWEVER, THR COULD ALSO BE A VAL. IN ADDITION, FIVE AMINO ACID RESIDUES IN THE ENZYME SEQUENCE HAVE ...Details: A TETRAPEPTIDE OF UNKNOWN SOURCE FOUND AT THE ACTIVE SITE REFINED BEST AS THR-ILE-THR-SER. HOWEVER, THR COULD ALSO BE A VAL. IN ADDITION, FIVE AMINO ACID RESIDUES IN THE ENZYME SEQUENCE HAVE BEEN REASSIGNED BASED ON THE ELECTRON DENSITY AT 1.8 A RESOLUTION; SEE SEQADV.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.52 Å2 / ksol: 0.303 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→27.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 12
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 28918 / σ(F): 2 / % reflection Rfree: 4.9 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.218 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.188 |