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Yorodumi- PDB-5n7q: CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n7q | ||||||
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Title | CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE INHIBITOR PEPSTATIN A | ||||||
Components |
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Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ixodes ricinus (castor bean tick) Actinobacteria (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 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 | 5n7q.cif.gz | 172.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n7q.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 5n7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n7q_validation.pdf.gz | 470.5 KB | Display | wwPDB validaton report |
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Full document | 5n7q_full_validation.pdf.gz | 474 KB | Display | |
Data in XML | 5n7q_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 5n7q_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/5n7q ftp://data.pdbj.org/pub/pdb/validation_reports/n7/5n7q | HTTPS FTP |
-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: 36787.234 Da / Num. of mol.: 2 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 #2: Protein/peptide | #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-GOL / | #5: 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 | Density Matthews: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1:1 PROTEIN (5 MG/ML IN 2.5 MM SODIUM FORMATE, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.14 M SODIUM CHLORIDE, 0.07 M BIS-TRIS, PH 5.5, 17.5% PEG3350, 1 MM DTT), CRYOCOOLED AFTER A QUICK SOAK ...Details: 1:1 PROTEIN (5 MG/ML IN 2.5 MM SODIUM FORMATE, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.14 M SODIUM CHLORIDE, 0.07 M BIS-TRIS, PH 5.5, 17.5% PEG3350, 1 MM DTT), CRYOCOOLED AFTER A QUICK SOAK IN RESERVOIR BUFFER + 30% PEG3350, 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: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.455→61.378 Å / Num. obs: 104842 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.455→1.53 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.227 / % possible all: 98.6 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→61.38 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.135 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.814 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→61.38 Å
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