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- PDB-7b2g: Crystal structure of R120Q GDAP1 mutant -

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Basic information

Entry
Database: PDB / ID: 7b2g
TitleCrystal structure of R120Q GDAP1 mutant
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsSIGNALING PROTEIN / Homodimer / mutant / mitochondria
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
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNguyen, G.T.T. / Sutinen, A. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: 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
DepositionNov 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2502
Polymers35,1581
Non-polymers921
Water00
1
A: Ganglioside-induced differentiation-associated protein 1
hetero molecules

A: Ganglioside-induced differentiation-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5004
Polymers70,3162
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1370 Å2
ΔGint-10 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.111, 148.111, 114.538
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

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


Mass: 35158.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: synthetic construct / Source: (gene. exp.) Homo sapiens (human) / Gene: GDAP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TB36
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
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: 6.22 Å3/Da / Density % sol: 80.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Succinic acid; 15% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→85.43 Å / Num. obs: 15366 / % possible obs: 99.9 % / Redundancy: 38.5 % / Biso Wilson estimate: 91.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.31
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1410 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AIA

7aia


Resolution: 3→85.43 Å / SU ML: 0.5719 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2642 1535 10 %
Rwork0.2298 13813 -
obs0.2329 15348 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.64 Å2
Refinement stepCycle: LAST / Resolution: 3→85.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 6 0 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022114
X-RAY DIFFRACTIONf_angle_d0.47962866
X-RAY DIFFRACTIONf_chiral_restr0.0356317
X-RAY DIFFRACTIONf_plane_restr0.002366
X-RAY DIFFRACTIONf_dihedral_angle_d21.6865800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.55721360.44321224X-RAY DIFFRACTION99.93
3.1-3.210.37331360.39171226X-RAY DIFFRACTION99.93
3.21-3.340.32761360.31871222X-RAY DIFFRACTION100
3.34-3.490.30461370.2931230X-RAY DIFFRACTION99.64
3.49-3.670.2861370.26551237X-RAY DIFFRACTION99.78
3.67-3.90.27991380.25911246X-RAY DIFFRACTION100
3.9-4.20.21491380.20481241X-RAY DIFFRACTION100
4.2-4.630.18981400.1941252X-RAY DIFFRACTION99.93
4.63-5.290.23711400.19721265X-RAY DIFFRACTION99.79
5.3-6.670.2861430.2231283X-RAY DIFFRACTION99.93
6.67-85.430.24731540.19171387X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 64.5370048195 Å / Origin y: -16.8249563556 Å / Origin z: 9.90204819568 Å
111213212223313233
T0.935973104543 Å20.17867134432 Å2-0.0317857165307 Å2-0.621648271139 Å20.000891157680746 Å2--0.721674998842 Å2
L2.50157469911 °20.737460641076 °2-0.164093431449 °2-3.91763224831 °2-0.498285476524 °2--4.31870601901 °2
S-0.0643744641543 Å °-0.125587998969 Å °-0.0204913756528 Å °-0.189390818595 Å °0.0314432690739 Å °0.232874717415 Å °-0.684228887233 Å °-0.374158943828 Å °0.0248662019802 Å °
Refinement TLS groupSelection details: all

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