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Yorodumi- PDB-5n71: CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n71 | ||||||
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Title | CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) | ||||||
Components | Putative cathepsin d | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ixodes ricinus (castor bean tick) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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 | 5n71.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n71.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n71_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 5n71_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 5n71_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 5n71_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/5n71 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/5n71 | 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
#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 (E. coli) / Strain (production host): BL21 / References: UniProt: V5HCK7 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-PEG / |
#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: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (6 MG/ML IN 2 MM BIS-TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG2000 MME), ...Details: CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (6 MG/ML IN 2 MM BIS-TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG2000 MME), CRYOCOOLED IN MOTHER LIQUOR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2015 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→49.08 Å / Num. obs: 36745 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.98 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.16 |
Reflection shell | Resolution: 1.88→1.99 Å / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.33 / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→49.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.131 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / 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: 32.146 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→49.08 Å
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Refine LS restraints |
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