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- PDB-7ywd: Human GDAP1 core domain, trigonal crystal form -

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Basic information

Entry
Database: PDB / ID: 7ywd
TitleHuman GDAP1 core domain, trigonal crystal form
ComponentsGanglioside-induced differentiation-associated protein 1
KeywordsMEMBRANE PROTEIN / GST homology / mitochondrial outer membrane / Charcot-Marie-Tooth disease
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 / Resolution: 3.2 Å
AuthorsRaasakka, 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
DepositionFeb 13, 2022Deposition 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,5304
Polymers127,5304
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)63,7652
Polymers63,7652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
2
B: Ganglioside-induced differentiation-associated protein 1
C: Ganglioside-induced differentiation-associated protein 1


Theoretical massNumber of molelcules
Total (without water)63,7652
Polymers63,7652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Ganglioside-induced differentiation-associated protein 1

D: Ganglioside-induced differentiation-associated protein 1


Theoretical massNumber of molelcules
Total (without water)63,7652
Polymers63,7652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)126.770, 126.770, 177.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 68 or resid 77 through 164 or resid 194 through 294))
d_2ens_1(chain "B" and (resid 23 through 164 or resid 194 through 294))
d_3ens_1(chain "C" and (resid 23 through 68 or resid 77 through 164 or resid 194 through 294))
d_4ens_1(chain "D" and (resid 23 through 68 or resid 77 through 164 or resid 194 through 294))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUPHEA1 - 46
d_12ens_1VALILEA52 - 139
d_13ens_1SERGLYA143 - 243
d_21ens_1GLUILEB1 - 134
d_22ens_1SERGLYB145 - 245
d_31ens_1GLUPHEC1 - 46
d_32ens_1VALILEC52 - 139
d_33ens_1SERGLYC148 - 248
d_41ens_1GLUPHED1 - 46
d_42ens_1VALILED53 - 140
d_43ens_1SERGLYD158 - 258

NCS oper:
IDCodeMatrixVector
1given(0.0539355227584, 0.993260131773, -0.102592738608), (0.95819430657, -0.0225706518608, 0.285226640643), (0.280988665683, -0.113687625997, -0.952953563115)63.9608543344, -55.8860331428, -79.7746140139
2given(-0.870891818274, 0.474928681203, 0.126452317634), (-0.488794389484, -0.810147941026, -0.323636151351), (-0.0512590057814, -0.343661259706, 0.937693688207)78.795022056, -88.5328835792, 29.5997250833
3given(0.438605056849, 0.783633317316, 0.43993684558), (-0.82694944876, 0.543577984372, -0.14379702397), (-0.351824122685, -0.300735430068, 0.886441192522)59.6946066373, 55.8179938245, 46.3209333323

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Components

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


Mass: 31882.412 Da / Num. of mol.: 4
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

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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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 200 mM NH4 formate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 27737 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 144.87 Å2 / CC1/2: 1 / Rrim(I) all: 0.107 / Net I/σ(I): 16
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4398 / CC1/2: 0.177 / Rrim(I) all: 3.874 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7alm

7alm


Resolution: 3.2→59.04 Å / SU ML: 0.6453 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.7106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2762 1360 4.91 %
Rwork0.2512 26326 -
obs0.2525 27686 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 188.43 Å2
Refinement stepCycle: LAST / Resolution: 3.2→59.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8225 0 0 0 8225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328403
X-RAY DIFFRACTIONf_angle_d0.607211361
X-RAY DIFFRACTIONf_chiral_restr0.03711258
X-RAY DIFFRACTIONf_plane_restr0.00431449
X-RAY DIFFRACTIONf_dihedral_angle_d15.98183221
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.25062894713
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.08000639321
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.69620160862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.45551270.41082581X-RAY DIFFRACTION99.85
3.31-3.450.42611370.38582588X-RAY DIFFRACTION99.89
3.45-3.60.38591310.40782598X-RAY DIFFRACTION99.93
3.6-3.790.39371370.34562606X-RAY DIFFRACTION99.78
3.79-4.030.32821360.30762607X-RAY DIFFRACTION99.56
4.03-4.340.29171400.27372605X-RAY DIFFRACTION100
4.34-4.780.26131380.24432614X-RAY DIFFRACTION100
4.78-5.470.28481380.24932655X-RAY DIFFRACTION100
5.47-6.890.30761320.28292680X-RAY DIFFRACTION100
6.89-59.040.21021440.18582792X-RAY DIFFRACTION99.8
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)
16.189923036190.9597892848710.4568042068222.681780156150.8418762574972.98817266220.5583943930140.3693486948420.4872679704540.04139137686-0.154091153568-0.392332581709-0.009461211518330.164751756257-0.4361117565551.481213796810.2865771607580.1114485025930.9345523782280.112091126151.1476615233242.4975558347-46.8668199844-43.9633755627
25.939050977780.547859086895-2.023763232744.88552161261.266353267166.059816204860.65164299265-0.6345806965020.76207227745-0.1897023638770.179929007328-0.593193841198-0.5846144896320.937903676884-0.7869582650421.19569751354-0.1348086069890.1634367791770.840570012983-0.2867627705071.2622747348224.4466577118-26.6912624491-20.2678871135
32.521974385890.5583880977170.5363776274287.6905947762-0.04800272045723.086381478280.582271141877-0.810361015559-0.9481790604161.00931560662-0.601051260323-0.7726372858880.4689108081330.4268815627250.04870130516971.21110625762-0.2705330103-0.2740571004371.535587164330.2779570731331.6226532975113.8993414038-57.01103333931.85285389869
43.74984078913-1.80260577188-0.6022939186893.343421686961.889996370792.987708783520.0623059524942-1.093763616471.02475803677-0.2788720088910.853993544182-1.26255492363-0.7742030075931.21609867832-0.774860820791.83810961724-0.5552270065850.2602131443872.09846073822-0.9726479618152.2416773198521.64249055011.523958763065.14255574168
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 23 - 294

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11(chain 'A' and resid 23 through 294)AA1 - 243
22(chain 'B' and resid 23 through 294)BB1 - 245
33(chain 'C' and resid 23 through 294)CC1 - 248
44(chain 'D' and resid 23 through 294)DD1 - 258

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