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Open data
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Basic information
Entry | Database: PDB / ID: 4qu8 | ||||||
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Title | Caspase-3 M61A V266H | ||||||
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![]() | hydrolase/hydrolase inhibitor / Allosteric Network / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cade, C. / Swartz, P.D. / MacKenzie, S.H. / Clark, A.C. | ||||||
![]() | ![]() Title: Modifying caspase-3 activity by altering allosteric networks. Authors: Cade, C. / Swartz, P. / MacKenzie, S.H. / Clark, A.C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.8 KB | Display | ![]() |
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PDB format | ![]() | 50.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qtxC ![]() 4qtyC ![]() 4qu0C ![]() 4qu5C ![]() 4qu9C ![]() 4quaC ![]() 4qubC ![]() 4qudC ![]() 4queC ![]() 4qugC ![]() 4quhC ![]() 4quiC ![]() 4qujC ![]() 4qulC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 31768.977 Da / Num. of mol.: 1 / Mutation: M61A V266H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | |
#3: Chemical | ChemComp-CL / ![]() |
#4: Chemical | ChemComp-DTT / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.94 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ...Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2011 | |||||||||||||||||||||
Radiation | Monochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||
Reflection | Resolution: 1.715→26.957 Å / Num. all: 29405 / Num. obs: 29405 / % possible obs: 98.79 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.715→26.957 Å
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Refine LS restraints |
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LS refinement shell |
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