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- PDB-8q8j: Crystal structure of human GPX4-R152H -

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Basic information

Entry
Database: PDB / ID: 8q8j
TitleCrystal structure of human GPX4-R152H
ComponentsGlutathione peroxidase
KeywordsOXIDOREDUCTASE / redox / ferroptosis / gpx4 / membrane associated / metabolism
Function / homology
Function and homology information


peroxidase activity / response to oxidative stress / mitochondrion
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione peroxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNapolitano, V. / Mourao, A. / Kolonko, M. / Bostock, M.J. / Sattler, M. / Conrad, M. / Popowicz, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human GPX4-R152H
Authors: Lorenz, S.M. / Wahida, A. / Emler, D. / Bostock, M. / Seibt, T. / Mourao, A. / Trumbach, D. / Rizzollo, F. / Napolitano, V. / Kolonko-Adamska, M. / Sommer, J. / Woo, M.S. / Rothammer, N. / ...Authors: Lorenz, S.M. / Wahida, A. / Emler, D. / Bostock, M. / Seibt, T. / Mourao, A. / Trumbach, D. / Rizzollo, F. / Napolitano, V. / Kolonko-Adamska, M. / Sommer, J. / Woo, M.S. / Rothammer, N. / Gaussman, S. / Alves, F. / Burkle, E. / Wanninger, J. / Boxleitner, K.M. / Stadler, M. / Doll, S. / Mishima, E. / Nakamura, T. / Maida, A. / Hass, D. / Escamilla-Ayala, A. / Puentes, L.P. / Lenberg, J. / Friedman, J. / Scale, C. / Proneth, B. / Henkelmann, L. / Aldrovandi, M. / Agostinis, P. / Zimprich, A. / Vogt-Weisenhorn, D. / Holter-Koch, S. / Lewerenz, J. / Steinacker, P. / Garcia-Saez, A.J. / Wurst, W. / Tietze, A. / Mann, M. / Westmeyer, G.G. / Friese, M.A. / Ramesh, S.K. / Wigby, K. / Sattler, M. / Ingold, I. / Ayton, S. / Jayavelu, A.K. / Popowicz, G. / Conrad, M.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione peroxidase


Theoretical massNumber of molelcules
Total (without water)18,9381
Polymers18,9381
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.871, 45.048, 82.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutathione peroxidase


Mass: 18937.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Production host: Escherichia coli (E. coli) / References: UniProt: K7ERP4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG monomethylether 5000 200 mM lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.05 Å / Num. obs: 8691 / % possible obs: 86.2 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 7.1
Reflection shellResolution: 2→8.9 Å / Num. unique obs: 671 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.59 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 34.04 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2463 422 4.86 %
Rwork0.2208 --
obs0.222 8680 83.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 0 47 1372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.887
X-RAY DIFFRACTIONf_dihedral_angle_d6.339189
X-RAY DIFFRACTIONf_chiral_restr0.059193
X-RAY DIFFRACTIONf_plane_restr0.006253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.290.30851360.27012838X-RAY DIFFRACTION88
2.29-2.880.31141510.27062732X-RAY DIFFRACTION85
2.88-39.590.20851350.19232688X-RAY DIFFRACTION79
Refinement TLS params.Method: refined / Origin x: 9.1288 Å / Origin y: 2.0252 Å / Origin z: 10.7485 Å
111213212223313233
T0.2517 Å20.0261 Å2-0.0532 Å2-0.2518 Å20 Å2--0.225 Å2
L4.4597 °20.4217 °20.3587 °2-3.4166 °20.4039 °2--3.0426 °2
S-0.0097 Å °-0.0956 Å °-0.0054 Å °-0.0364 Å °0.0062 Å °0.003 Å °-0.0561 Å °-0.0457 Å °0.0221 Å °
Refinement TLS groupSelection details: (chain A and resseq 6:170)

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