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Yorodumi- PDB-5yq8: Crystal structure of retroviral protease-like domain of Ddi1 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yq8 | ||||||
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Title | Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major | ||||||
Components | DNA-damage inducible protein DDI1-like protein | ||||||
Keywords | HYDROLASE / retropepsin / aspartic protease / cytoplasmic | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Suguna, K. / Kumar, S. | ||||||
Funding support | India, 1items
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Citation | Journal: FEBS Open Bio / Year: 2018 Title: Crystal structure of the retroviral protease-like domain of a protozoal DNA damage-inducible 1 protein. Authors: Kumar, S. / Suguna, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yq8.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yq8.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 5yq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yq8 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yq8 | HTTPS FTP |
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-Related structure data
Related structure data | 5ys4C 2i1aS S: Starting model for refinement C: citing same article (ref.) |
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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 | Mass: 14560.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_01_0610 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9AC52, UniProt: I7HUG0*PLUS #2: 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: 2.1 Å3/Da / Density % sol: 41.4 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 4.5 Details: 0.1 M sodium acetate trihydrate, 30 % polyethylene glycol 1500 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.25→58.55 Å / Num. obs: 22170 / % possible obs: 96.76 % / Redundancy: 2.6 % / CC1/2: 0.971 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.136 / Net I/σ(I): 5.9 | |||||||||||||||
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2068 / CC1/2: 0.324 / Rpim(I) all: 0.339 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I1A Resolution: 2.25→42.72 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.835 / SU B: 4.305 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.054 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.669 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→42.72 Å
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Refine LS restraints |
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