+Open data
-Basic information
Entry | Database: PDB / ID: 6wi4 | ||||||
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Title | Caspases from Scleractinian Coral | ||||||
Components |
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Keywords | CELL CYCLE / caspase / coral apoptosis / functional divergence / substrate selection / card-caspase | ||||||
Biological species | Porites astreoides (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Clark, A.C. / Swartz, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Caspases from scleractinian coral show unique regulatory features. Authors: Shrestha, S. / Tung, J. / Grinshpon, R.D. / Swartz, P. / Hamilton, P.T. / Dimos, B. / Mydlarz, L. / Clark, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wi4.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wi4.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 6wi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wi4_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 6wi4_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 6wi4_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 6wi4_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/6wi4 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/6wi4 | HTTPS FTP |
-Related structure data
Related structure data | 2j30S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26851.572 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porites astreoides (invertebrata) / Production host: Escherichia coli (E. coli) #2: Protein/peptide | | Mass: 755.882 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porites astreoides (invertebrata) / Production host: Escherichia coli (E. coli) #3: Protein/peptide | Mass: 502.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porites astreoides (invertebrata) / Production host: Escherichia coli (E. coli) #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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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: 2.73 Å3/Da / Density % sol: 54.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Protein crystalized in a solution of 0.1 M sodium malonate pH 5.0, 12% w/v polyethylene glycol (PEG) 3350, and conditions were optimized such that the best diffracting crystals of PaCasp7a ...Details: Protein crystalized in a solution of 0.1 M sodium malonate pH 5.0, 12% w/v polyethylene glycol (PEG) 3350, and conditions were optimized such that the best diffracting crystals of PaCasp7a were obtained at 18 C in a solution of 0.1 M sodium malonate, pH 4.9-5.1, 15-17% PEG 3350 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals for PaCasp7a appeared within 3 to 5 days and were briefly immersed in a cryogenic solution containing 20% PEG 4000, 80% reservoir solution PH range: 4.9 - 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: Temperature control: Constant temperature Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Insertion Device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→50 Å / Num. obs: 84182 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.117 / Rrim(I) all: 0.249 / Χ2: 1.484 / Net I/σ(I): 9 / Num. measured all: 415894 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J30 Resolution: 1.57→39.4 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.52 Å2 / Biso mean: 17.6375 Å2 / Biso min: 6.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→39.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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