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Yorodumi- PDB-5n70: CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n70 | ||||||
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Title | CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE N-TERMINAL OCTAPEPTIDE OF THE PROPEPTID | ||||||
Components |
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Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ixodes ricinus (castor bean tick) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 Å | ||||||
Authors | Brynda, J. / Hanova, I. / Hobizalova, R. / Mares, M. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2018 Title: Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite. Authors: Hanova, I. / Brynda, J. / Houstecka, R. / Alam, N. / Sojka, D. / Kopacek, P. / Maresova, L. / Vondrasek, J. / Horn, M. / Schueler-Furman, O. / Mares, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n70.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n70.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/5n70 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/5n70 | HTTPS FTP |
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-Related 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 | Mass: 37615.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: V5HCK7 |
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#2: Protein/peptide | Mass: 975.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Ixodes ricinus (castor bean tick) / References: UniProt: A4GTA5*PLUS |
#3: 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: 2.18 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (5 MG/ML IN 5 MM TRIS-HCL, REMARK 280 PH 7.0, 10% DMSO) TO RESERVOIR (0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, 30% PEG8000), CRYOCOOLED ...Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (5 MG/ML IN 5 MM TRIS-HCL, REMARK 280 PH 7.0, 10% DMSO) TO RESERVOIR (0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, 30% PEG8000), CRYOCOOLED AFTER A QUICK SOAK IN RESERVOIR BUFFER + 25% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979402 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979402 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.2 Å / Num. obs: 30080 / % possible obs: 99.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.18 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.43 / % possible all: 96.5 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.81→45.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.294 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.517 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→45.2 Å
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Refine LS restraints |
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