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Open data
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Basic information
Entry | Database: PDB / ID: 7alm | ||||||
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Title | Crystal structure of human GDAP1 at 2.8 Angstrom resolution. | ||||||
![]() | Ganglioside-induced differentiation-associated protein 1 | ||||||
![]() | SIGNALING PROTEIN / Outer mitochondrial membrane protein / Charcot-Marie-Tooth | ||||||
Function / homology | ![]() Class I peroxisomal membrane protein import / cellular response to vitamin D / protein targeting to mitochondrion / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / membrane ...Class I peroxisomal membrane protein import / cellular response to vitamin D / protein targeting to mitochondrion / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, G.T.T. / Sutinen, A. / Raasakka, A. / Kursula, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Complete Dimeric Human GDAP1 Core Domain Provides Insights into Ligand Binding and Clustering of Disease Mutations. Authors: Nguyen, G.T.T. / Sutinen, A. / Raasakka, A. / Muruganandam, G. / Loris, R. / Kursula, P. #1: ![]() Title: Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told". Authors: Grzechowiak, M. / Sekula, B. / Jaskolski, M. / Ruszkowski, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354 KB | Display | ![]() |
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PDB format | ![]() | 256 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437 KB | Display | ![]() |
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Full document | ![]() | 439.6 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aiaC C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32774.438 Da / Num. of mol.: 2 / Mutation: No mutations 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: 4.32 Å3/Da / Density % sol: 71.56 % / Description: tetrahedral |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate, 20 % PEG3350 / Temp details: cold room |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2019 / Details: double crystal silicon monochromator |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.36 Å / Num. obs: 24883 / % possible obs: 99.62 % / Redundancy: 2 % / Biso Wilson estimate: 57.52 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Rrim(I) all: 0.056 / Χ2: 0.91 / Net I/σ(I): 11.55 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 3571 / CC1/2: 0.854 / CC star: 0.965 / Rpim(I) all: 0.362 / Rrim(I) all: 0.512 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 79.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→42.36 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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