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- PDB-7qp0: Crystal structure of metacaspase from candida glabrata with magnesium -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qp0 | ||||||
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Title | Crystal structure of metacaspase from candida glabrata with magnesium | ||||||
![]() | Metacaspase-1 | ||||||
![]() | APOPTOSIS / METACASPASE / PROTEASE / CA2+-DEPENDENT ACTIVATION | ||||||
Function / homology | calcium-dependent cysteine-type endopeptidase activity / Caspase-like domain superfamily / protein quality control for misfolded or incompletely synthesized proteins / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / apoptotic process / nucleus / cytosol / Metacaspase-1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Conchou, L. / Ballut, L. / Violot, S. / Aghajari, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and molecular determinants of Candida glabrata metacaspase maturation and activation by calcium. Authors: Conchou, L. / Doumeche, B. / Galisson, F. / Violot, S. / Dugelay, C. / Diesis, E. / Page, A. / Bienvenu, A.L. / Picot, S. / Aghajari, N. / Ballut, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137 KB | Display | ![]() |
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PDB format | ![]() | 102.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qp1C ![]() 4f6oS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 43844.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6FPX9, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.97 % |
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Crystal grow | Temperature: 292 K / Method: evaporation / pH: 7.6 / Details: 0.2 M Mg Acetate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.38 Å / Num. obs: 87056 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rrim(I) all: 0.103 / Net I/σ(I): 8.44 |
Reflection shell | Resolution: 1.6→1.8 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 25834 / CC1/2: 0.76 / Rrim(I) all: 0.859 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4F6O Resolution: 1.6→38.38 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.37 / 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: 119.03 Å2 / Biso mean: 27.6477 Å2 / Biso min: 10.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→38.38 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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