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- PDB-6uih: Crystal structure of the core domain from the GST-like protein GDAP1 -

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Basic information

Entry
Database: PDB / ID: 6uih
TitleCrystal structure of the core domain from the GST-like protein GDAP1
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsSIGNALING PROTEIN / thioredoxin / GST-like / GDAP1 / mitochondrial morphology
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / cellular response to vitamin D / protein targeting to mitochondrion / mitochondrial fission / mitochondrial fusion / response to retinoic acid / mitochondrial outer membrane / cytosol
Similarity search - Function
Ganglioside-induced differentiation-associated protein 1 / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Ganglioside-induced differentiation-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.826 Å
AuthorsGoogins, M.R. / VanDemark, A.P.
CitationJournal: Faseb J. / Year: 2020
Title: Structural and functional divergence of GDAP1 from the glutathione S-transferase superfamily.
Authors: Googins, M.R. / Woghiren-Afegbua, A.O. / Calderon, M. / St Croix, C.M. / Kiselyov, K.I. / VanDemark, A.P.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ganglioside-induced differentiation-associated protein 1


Theoretical massNumber of molelcules
Total (without water)26,8321
Polymers26,8321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.598, 196.598, 196.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Ganglioside-induced differentiation-associated protein 1 / GDAP1


Mass: 26831.730 Da / Num. of mol.: 1 / Fragment: GST-like core domain
Source method: isolated from a genetically manipulated source
Details: amino acids 145-199 replaced with GTG-linker / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gdap1 / Plasmid: pKF3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RIPL / References: UniProt: O88741
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.9 Å3/Da / Density % sol: 79.15 % / Mosaicity: 0.09 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 1.0M Citrate, 200mM NaCl, 10mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.826→98.3 Å / Num. obs: 15877 / % possible obs: 100 % / Redundancy: 70.1 % / CC1/2: 1 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.013 / Rrim(I) all: 0.108 / Net I/σ(I): 37.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.83-2.98761.98617216422650.9120.2281.9992.9100
8.94-98.360.20.0543524858610.0070.05492.899.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.826→49.149 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.9
RfactorNum. reflection% reflection
Rfree0.2235 1200 7.56 %
Rwork0.2112 --
obs0.2121 15869 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.01 Å2 / Biso mean: 98.7738 Å2 / Biso min: 54.61 Å2
Refinement stepCycle: final / Resolution: 2.826→49.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 0 0 1634
Num. residues----198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.826-2.9390.39411200.35861609
2.939-3.07280.31951200.29891614
3.0728-3.23470.30271720.26891548
3.2347-3.43740.29021280.24471603
3.4374-3.70270.27581200.22371634
3.7027-4.07510.21771200.2061621
4.0751-4.66440.20171200.17021644
4.6644-5.87510.21881800.1891611
5.8751-49.1490.17981200.2111785

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