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- PDB-7q6k: Crystal structure of the human GDAP1 CMT2 mutant-R120W -

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Basic information

Entry
Database: PDB / ID: 7q6k
TitleCrystal structure of the human GDAP1 CMT2 mutant-R120W
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsSIGNALING PROTEIN / Charcot-Marie-Tooth / CMT2 / Mutation / 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, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 / molecular replacement / Resolution: 3.41 Å
AuthorsSutinen, A. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland24302881 Finland
CitationJournal: Febs Open Bio / Year: 2022
Title: Structural insights into Charcot-Marie-Tooth disease-linked mutations in human GDAP1.
Authors: Sutinen, A. / Nguyen, G.T.T. / Raasakka, A. / Muruganandam, G. / Loris, R. / Ylikallio, E. / Tyynismaa, H. / Bartesaghi, L. / Ruskamo, S. / Kursula, P.
History
DepositionNov 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)32,8031
Polymers32,8031
Non-polymers00
Water0
1
A: Ganglioside-induced differentiation-associated protein 1

A: Ganglioside-induced differentiation-associated protein 1


Theoretical massNumber of molelcules
Total (without water)65,6072
Polymers65,6072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area1340 Å2
ΔGint-14 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.270, 147.270, 114.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 32803.453 Da / Num. of mol.: 1 / Mutation: R120W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDAP1 / Plasmid: pTH-27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TB36

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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: 5.47 Å3/Da / Density % sol: 80.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 6000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationMonochromator: double crystal silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.41→48.21 Å / Num. obs: 10468 / % possible obs: 99.9 % / Redundancy: 12.816 % / Biso Wilson estimate: 91.583 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.388 / Rrim(I) all: 0.404 / Χ2: 0.697 / Net I/σ(I): 6.54 / Num. measured all: 134163 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.41-3.512.5033.9770.8194907617590.5394.14799.7
3.5-3.5913.072.361.596467397380.9422.45799.9
3.59-3.713.8312.0081.7796406976970.7582.085100
3.7-3.8113.7041.6922.1196347037030.7211.758100
3.81-3.9413.5771.3552.5991516746740.8771.409100
3.94-4.0713.5180.9663.588276546530.931.00499.8
4.07-4.2313.3230.7944.1385006386380.9520.826100
4.23-4.413.0380.7054.6679146076070.9370.734100
4.4-4.612.4770.5195.7573495895890.9710.541100
4.6-4.8211.9880.5325.6367855665660.9610.556100
4.82-5.0812.8390.4227.0469975455450.9880.439100
5.08-5.3911.9860.3587.360175025020.9880.374100
5.39-5.7613.3390.3987.2964964874870.9880.414100
5.76-6.2213.1320.367.9660544624610.9880.37499.8
6.22-6.8212.8120.3249.1253814204200.9850.338100
6.82-7.6212.3120.21211.8547403853850.9930.221100
7.62-8.811.0770.11518.2238883513510.9960.121100
8.8-10.7811.2770.07625.2233833003000.9970.08100
10.78-15.2511.4440.06928.5727812432430.9980.072100
15.25-48.219.9330.0626.4314901591500.9960.06494.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.41 Å48.15 Å
Translation3.41 Å48.15 Å

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Processing

Software
NameVersionClassification
PHENIXdev_3928refinement
XDSFeb 5, 2021data reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ALM

7alm


Resolution: 3.41→48.21 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2935 524 5.02 %
Rwork0.2525 9907 -
obs0.2545 10431 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 312.44 Å2 / Biso mean: 132.38 Å2 / Biso min: 60.77 Å2
Refinement stepCycle: final / Resolution: 3.41→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 0 0 2051
Num. residues----248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.41-3.750.35371260.3462391251799
3.75-4.290.30931290.288724362565100
4.29-5.410.30411300.255324642594100
5.41-48.210.26391390.212626162755100

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