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- PDB-6elw: High resolution structure of selenocysteine containing human GPX4 -

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Basic information

Entry
Database: PDB / ID: 6elw
TitleHigh resolution structure of selenocysteine containing human GPX4
ComponentsPhospholipid hydroperoxide glutathione peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / HUMAN GPX4 / PEROXIDASE / SELENOPROTEIN / THIOREDOXIN-FOLD / ANTI-OXIDATVE DEFENSE SYSTEM
Function / homology
Function and homology information


phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / glutathione peroxidase activity / long-chain fatty acid biosynthetic process / protein polymerization / phospholipid metabolic process / response to estradiol / nuclear envelope / chromatin organization / cellular response to oxidative stress / spermatogenesis / response to oxidative stress / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
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. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phospholipid hydroperoxide glutathione peroxidase GPX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKalms, J. / Borchert, A. / Kuhn, H. / Scheerer, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationSFB740 Germany
German Research FoundationSFB1078 Germany
German Research FoundationKu961/11-1 Germany
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Crystal structure and functional characterization of selenocysteine-containing glutathione peroxidase 4 suggests an alternative mechanism of peroxide reduction.
Authors: Borchert, A. / Kalms, J. / Roth, S.R. / Rademacher, M. / Schmidt, A. / Holzhutter, H.G. / Kuhn, H. / Scheerer, P.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9134
Polymers21,8071
Non-polymers1063
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-28 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.963, 69.000, 35.666
Angle α, β, γ (deg.)90.00, 115.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phospholipid hydroperoxide glutathione peroxidase, mitochondrial / PHGPx / Glutathione peroxidase 4 / GSHPx-4


Mass: 21806.602 Da / Num. of mol.: 1 / Mutation: C2A, C10A, C37S, Sec46U, C76A, C85S, C107A, C148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Plasmid: pET-15b-cGPX4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): selB:kan cys51E
References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1.7 Å3/Da / Density % sol: 27.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 % (w/v) PEG 1500, 10 % (v/v) isopropanol, 0.1 M calcium chloride and 0.1 M imidazole/ hydrochloric acid pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 6, 2015 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.3→34.52 Å / Num. obs: 35608 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OBI

2obi


Resolution: 1.3→34.52 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.7 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15541 1678 4.7 %RANDOM
Rwork0.1238 ---
obs0.12526 33903 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.53 Å2
2---0.72 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 3 210 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191436
X-RAY DIFFRACTIONr_bond_other_d0.0030.021326
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.941943
X-RAY DIFFRACTIONr_angle_other_deg1.20133091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27124.47867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86815255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.694156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211632
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02306
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1851.009703
X-RAY DIFFRACTIONr_mcbond_other1.1531.006702
X-RAY DIFFRACTIONr_mcangle_it1.5361.517888
X-RAY DIFFRACTIONr_mcangle_other1.5371.52889
X-RAY DIFFRACTIONr_scbond_it2.0731.29733
X-RAY DIFFRACTIONr_scbond_other2.0721.29734
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5051.8261056
X-RAY DIFFRACTIONr_long_range_B_refined4.5514.3111707
X-RAY DIFFRACTIONr_long_range_B_other3.70813.4121660
X-RAY DIFFRACTIONr_rigid_bond_restr1.64132762
X-RAY DIFFRACTIONr_sphericity_free25.8955150
X-RAY DIFFRACTIONr_sphericity_bonded8.44852789
LS refinement shellResolution: 1.297→1.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 144 -
Rwork0.225 2347 -
obs--94.68 %

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