+Open data
-Basic information
Entry | Database: PDB / ID: 6pdq | ||||||
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Title | Ancestral Effector Caspase 3/6/7 | ||||||
Components |
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Keywords | APOPTOSIS / Ancestral Effector Caspase / protease / ancestral protein reconstruction | ||||||
Function / homology | Caspase-like / Rossmann fold - #1460 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Clark, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochem.J. / Year: 2019 Title: Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity. Authors: Grinshpon, R.D. / Shrestha, S. / Titus-McQuillan, J. / Hamilton, P.T. / Swartz, P.D. / 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 | 6pdq.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pdq.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 6pdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/6pdq ftp://data.pdbj.org/pub/pdb/validation_reports/pd/6pdq | HTTPS FTP |
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-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: 16070.114 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 10561.993 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.04 Å3/Da / Density % sol: 39.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, pH 4.6, 0.1 M sodium acetate trihydrate, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→43.493 Å / Num. obs: 39730 / % possible obs: 99.23 % / Redundancy: 7 % / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.83→1.89 Å / Num. unique obs: 3741 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→43.493 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→43.493 Å
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Refine LS restraints |
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LS refinement shell |
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