+Open data
-Basic information
Entry | Database: PDB / ID: 8a4j | ||||||
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Title | Human GDAP1, A247V mutant | ||||||
Components | Ganglioside-induced differentiation-associated protein 1 | ||||||
Keywords | MEMBRANE PROTEIN / GST family / mitochondria / disease mutation / dimer | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Sutinen, A. / Kursula, P. | ||||||
Funding support | Finland, 1items
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Citation | Journal: Plos One / Year: 2023 Title: Conserved intramolecular networks in GDAP1 are closely connected to CMT-linked mutations and protein stability. Authors: Sutinen, A. / Paffenholz, D. / Nguyen, G.T.T. / Ruskamo, S. / Torda, A.E. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a4j.cif.gz | 364.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a4j.ent.gz | 251.7 KB | Display | PDB format |
PDBx/mmJSON format | 8a4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/8a4j ftp://data.pdbj.org/pub/pdb/validation_reports/a4/8a4j | HTTPS FTP |
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-Related structure data
Related structure data | 7b2gC 8a4kC 7almS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.848031280417, 0.528413984447, -0.0402692000905), (0.529608319266, 0.847753273135, -0.0287995842625), (0.0189202431127, -0.0457498516957, -0.998773735873)Vector: 33. ...NCS oper: (Code: given Matrix: (-0.848031280417, 0.528413984447, -0.0402692000905), Vector: |
-Components
#1: Protein | Mass: 32802.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GDAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TB36 #2: Water | ChemComp-HOH / | |
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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: 3.75 Å3/Da / Density % sol: 67.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.15 M DL-malic acid (pH 7.3), 20% (w/v) PEG3500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→50 Å / Num. obs: 28237 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.091 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.68→2.84 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.627 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 4457 / CC1/2: 0.814 / Rrim(I) all: 169 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ALM Resolution: 2.68→42.28 Å / SU ML: 0.4873 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2807 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→42.28 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.87068764288 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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