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Open data
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Basic information
Entry | Database: PDB / ID: 4d2k | ||||||
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Title | Crystal structure of DREP2 CIDE domain | ||||||
![]() | DREP2 | ||||||
![]() | APOPTOSIS / ENERGY METABOLISM / DNA FRAGMENTATION FACTOR (DFF) | ||||||
Function / homology | ![]() : / : / synaptic membrane / postsynaptic membrane / regulation of apoptotic process / apoptotic process / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jang, T.H. / Park, H.H. / Kim, Y.G. / Jeong, J.H. | ||||||
![]() | ![]() Title: CIDE domains form functionally important higher-order assemblies for DNA fragmentation. Authors: Choi, J.Y. / Qiao, Q. / Hong, S.H. / Kim, C.M. / Jeong, J.H. / Kim, Y.G. / Jung, Y.K. / Wu, H. / Park, H.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.7 KB | Display | ![]() |
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PDB format | ![]() | 57.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.9 KB | Display | ![]() |
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Full document | ![]() | 447.5 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xpcC ![]() 2eelS S: Starting model for refinement 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10063.541 Da / Num. of mol.: 4 / Fragment: CIDE DOMAIN, RESIDUES 1-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.3 % / Description: NONE |
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Crystal grow | pH: 6.2 Details: 100 MM BIS-TRIS PH6.2, 300 MM MAGNESIUM FORMATE DIHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22067 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.2 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2EEL Resolution: 2.302→33.263 Å / SU ML: 0.29 / σ(F): 1.52 / Phase error: 24.71 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.302→33.263 Å
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Refine LS restraints |
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LS refinement shell |
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