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- PDB-5l71: Crystal structure of mouse phospholipid hydroperoxide glutathione... -

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Basic information

Entry
Database: PDB / ID: 5l71
TitleCrystal structure of mouse phospholipid hydroperoxide glutathione peroxidase 4 (GPx4)
ComponentsPhospholipid hydroperoxide glutathione peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / phospholipid hydroperoxide glutathione peroxidase 4 (GPx4) / selenocysteine
Function / homology
Function and homology information


Synthesis of 12-eicosatetraenoic acid derivatives / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / negative regulation of ferroptosis / selenium binding / Synthesis of 15-eicosatetraenoic acid derivatives ...Synthesis of 12-eicosatetraenoic acid derivatives / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / negative regulation of ferroptosis / selenium binding / Synthesis of 15-eicosatetraenoic acid derivatives / lipoxygenase pathway / : / arachidonic acid metabolic process / multicellular organism development / glutathione peroxidase activity / protein polymerization / glutathione metabolic process / peroxidase activity / response to estradiol / nuclear envelope / chromatin organization / regulation of inflammatory response / spermatogenesis / mitochondrial inner membrane / response to oxidative stress / protein-containing complex / mitochondrion / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJanowski, R. / Scanu, S. / Madl, T. / Niessing, D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal and solution structural studies of mouse phospholipid hydroperoxide glutathione peroxidase 4.
Authors: Janowski, R. / Scanu, S. / Niessing, D. / Madl, T.
History
DepositionJun 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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)19,7464
Polymers19,5601
Non-polymers1863
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint8 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.260, 61.260, 113.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 19559.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpx4 / Production host: Escherichia coli (E. coli)
References: UniProt: O70325, phospholipid-hydroperoxide glutathione peroxidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 292 K / Method: small tubes / pH: 6.5 / Details: 100 mM MES, 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 23549 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 4.09 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OBI

2obi


Resolution: 1.8→53.05 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.985 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19264 1251 5.3 %RANDOM
Rwork0.15065 ---
obs0.15305 22298 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.46 Å20 Å2
2--0.91 Å2-0 Å2
3----2.95 Å2
Refinement stepCycle: 1 / Resolution: 1.8→53.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 12 185 1522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0191395
X-RAY DIFFRACTIONr_bond_other_d0.0020.021308
X-RAY DIFFRACTIONr_angle_refined_deg2.4631.9441884
X-RAY DIFFRACTIONr_angle_other_deg1.2533020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1275174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.224.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44515244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.544158
X-RAY DIFFRACTIONr_chiral_restr0.1940.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
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_it2.2152.016669
X-RAY DIFFRACTIONr_mcbond_other2.2152.016668
X-RAY DIFFRACTIONr_mcangle_it3.2773.006837
X-RAY DIFFRACTIONr_mcangle_other3.2753.007838
X-RAY DIFFRACTIONr_scbond_it3.3882.386726
X-RAY DIFFRACTIONr_scbond_other3.3782.385726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1923.4061043
X-RAY DIFFRACTIONr_long_range_B_refined8.418.6641731
X-RAY DIFFRACTIONr_long_range_B_other8.39818.6881732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 94 -
Rwork0.216 1600 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: -27.1232 Å / Origin y: 21.0802 Å / Origin z: -3.4249 Å
111213212223313233
T0.2378 Å2-0.0369 Å20.0593 Å2-0.079 Å20.0025 Å2--0.069 Å2
L0.6303 °20.2069 °20.1531 °2-0.1137 °2-0.0831 °2--1.953 °2
S0.0678 Å °-0.1281 Å °-0.1356 Å °-0.0436 Å °-0.0009 Å °-0.0755 Å °-0.235 Å °-0.2753 Å °-0.0669 Å °

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