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- PDB-7alm: Crystal structure of human GDAP1 at 2.8 Angstrom resolution. -

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Basic information

Entry
Database: PDB / ID: 7alm
TitleCrystal structure of human GDAP1 at 2.8 Angstrom resolution.
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsSIGNALING PROTEIN / Outer mitochondrial membrane protein / Charcot-Marie-Tooth
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / cellular response to vitamin D / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / protein targeting to mitochondrion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / nucleus ...Class I peroxisomal membrane protein import / cellular response to vitamin D / mitochondrial fission / peroxisomal membrane / mitochondrial fusion / protein targeting to mitochondrion / response to retinoic acid / mitochondrial outer membrane / mitochondrion / nucleus / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsNguyen, G.T.T. / Sutinen, A. / Raasakka, A. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
Citation
Journal: Front Mol Biosci / Year: 2020
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: Journal: Acta Biochim.Pol. / Year: 2021
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
DepositionOct 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,5492
Polymers65,5492
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Purified protein samples were analyzed with SDS-PAGE, and then selected bands were identified with MALDI-TOF MS/MS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-10 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.808, 115.878, 116.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 32774.438 Da / Num. of mol.: 2 / Mutation: No mutations
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 4.32 Å3/Da / Density % sol: 71.56 % / Description: tetrahedral
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate, 20 % PEG3350 / Temp details: cold room

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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 PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2019 / Details: double crystal silicon monochromator
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.18_3861refinement
PHENIX1.18_3861refinement
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→42.36 Å / SU ML: 0.4473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 1251 5.03 %
Rwork0.2426 23614 -
obs0.2436 24865 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 0 39 4012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224096
X-RAY DIFFRACTIONf_angle_d0.46235547
X-RAY DIFFRACTIONf_chiral_restr0.0363619
X-RAY DIFFRACTIONf_plane_restr0.0024698
X-RAY DIFFRACTIONf_dihedral_angle_d17.97151557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.910.39991380.34092587X-RAY DIFFRACTION99.71
2.91-3.040.34171360.3212593X-RAY DIFFRACTION99.85
3.04-3.210.36821360.31732571X-RAY DIFFRACTION99.82
3.21-3.410.29981380.27372573X-RAY DIFFRACTION99.67
3.41-3.670.25621390.25222628X-RAY DIFFRACTION99.82
3.67-4.040.2591390.23542619X-RAY DIFFRACTION99.93
4.04-4.620.2211380.20012615X-RAY DIFFRACTION99.78
4.62-5.820.22341420.2082661X-RAY DIFFRACTION99.36
5.82-42.360.24051450.232767X-RAY DIFFRACTION99.05
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.01761399286-3.46566283738-0.3023002827344.544000395321.555138470037.629535615680.1405433626530.2010490464620.461312179111-0.228257809953-0.0341254328581-0.00345813215233-0.34798338928-0.170967557629-0.105911148990.308770362438-0.02979117836780.01107407946430.3462931445420.05933790412310.45518575853628.1125260054-5.11049278669-9.20513741966
27.19531949856-0.272504624291-3.818665972961.77924311180.8141393804855.28809371876-0.05930961706490.161651701177-0.428889943110.344057504953-0.2082173135680.2677902222440.351996164937-0.6550452524790.2423637654480.40588977698-0.0375574099662-0.02779592726140.391275774172-0.006353029013260.43442587651825.7741672972-22.26922254287.14769622495
36.9469842951-1.49620526447-2.153231416634.413141250060.6449265624055.996757010390.136226489661-0.225198705361-0.07622018544530.123890984246-0.188684159096-0.49422981875-0.03234597421060.3356668429470.02928086567870.299201343545-0.0475443833908-0.07826786273250.2896086663210.02364230365740.37933773255940.3942923089-14.34250795512.0718598073
47.50598979751-0.399854532166-0.1474756759493.926060026910.687337452724.201264109730.078679338068-0.501949811820.07237812932820.1659916415680.09133613450540.129905130068-0.277587809569-1.17800972024-0.05652657029420.4577185362510.1048101780180.05699319606630.7691405768070.170173575290.5102741266447.10855114050.456837385412-14.1990878307
51.94930955742-0.4769052579931.199654209682.26197397155-0.9316381910634.945365063480.234092921349-0.933398882609-0.566100188364-0.1945863716360.03086083441450.4673505159821.21486986506-1.93188286993-0.114601783490.766088934905-0.395468796099-0.05951882893891.254730426090.2952008018820.690004386413-4.46310343944-7.71028605313-27.0300285132
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 23 through 117 )AA23 - 1171 - 93
22chain 'A' and (resid 118 through 229 )AA118 - 22994 - 182
33chain 'A' and (resid 230 through 302 )AA230 - 302183 - 255
44chain 'B' and (resid 23 through 117 )BB23 - 1171 - 93
55chain 'B' and (resid 118 through 302 )BB118 - 30294 - 230

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