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- PDB-2obi: Crystal structure of the Selenocysteine to Cysteine Mutant of hum... -

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Basic information

Entry
Database: PDB / ID: 2obi
TitleCrystal structure of the Selenocysteine to Cysteine Mutant of human phospholipid hydroperoxide glutathione peroxidase (GPx4)
ComponentsPhospholipid hydroperoxide glutathione peroxidase (GPX4)
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 / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / arachidonate metabolic process / Biosynthesis of aspirin-triggered D-series resolvins ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / arachidonate 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 / negative regulation of ferroptosis / protein polymerization / phospholipid metabolic process / response to estradiol / nuclear envelope / chromatin organization / 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: 1.55 Å
AuthorsScheerer, P. / Krauss, N. / Hoehne, W.
CitationJournal: Biochemistry / Year: 2007
Title: Structural basis for catalytic activity and enzyme polymerization of phospholipid hydroperoxide glutathione peroxidase-4 (GPx4).
Authors: Scheerer, P. / Borchert, A. / Krauss, N. / Wessner, H. / Gerth, C. / Hohne, W. / Kuhn, H.
History
DepositionDec 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase (GPX4)


Theoretical massNumber of molelcules
Total (without water)20,9551
Polymers20,9551
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.362, 61.362, 113.891
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 (GPX4) / PHGPx / GPX-4


Mass: 20955.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 8000, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 29, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 35135 / Num. obs: 35135 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 32.07
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.0364 / Mean I/σ(I) obs: 2.48 / Num. unique all: 2429 / Rsym value: 0.0364 / % possible all: 66.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GP1

1gp1


Resolution: 1.55→30.69 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 1761 -RANDOM
Rwork0.1641 ---
all0.1652 33339 --
obs0.1652 33339 95.6 %-
Displacement parametersBiso mean: 8.514 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.063 Å0.062 Å
Luzzati d res low-6 Å
Luzzati sigma a-0.041 Å
Refinement stepCycle: LAST / Resolution: 1.55→30.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 0 151 1498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.015
X-RAY DIFFRACTIONr_angle_refined_deg1.276
LS refinement shellResolution: 1.55→1.59 Å
RfactorNum. reflection% reflection
Rfree0.293 1599 -
Rwork0.25 --
obs-1599 94 %

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