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- PDB-2gs3: Crystal structure of the selenocysteine to glycine mutant of huma... -

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Basic information

Entry
Database: PDB / ID: 2gs3
TitleCrystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4)
ComponentsPhospholipid hydroperoxide glutathione peroxidase
KeywordsOXIDOREDUCTASE / GPX4 / GSHPX-4 / phospholipid hydroperoxide / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / negative regulation of ferroptosis / Synthesis of 12-eicosatetraenoic acid derivatives / 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 / negative regulation of ferroptosis / Synthesis of 12-eicosatetraenoic acid derivatives / 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 / 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: 1.9 Å
AuthorsJohansson, C. / Kavanagh, K.L. / Rojkova, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4)
Authors: Johansson, C. / Kavanagh, K.L. / Rojkova, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2202
Polymers21,1841
Non-polymers351
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.945, 62.945, 195.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phospholipid hydroperoxide glutathione peroxidase / PHGPx / GPX-4


Mass: 21184.301 Da / Num. of mol.: 1 / Mutation: SeCys73Gly
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 4.58 Å3/Da / Density % sol: 73.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 20% PEG 3350, 0.2 M ammonium chloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 32109 / Num. obs: 32109 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4550 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F8A

2f8a


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.242 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 1487 4.6 %RANDOM
Rwork0.17163 ---
all0.17251 30562 --
obs0.17251 30562 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.285 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 1 130 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221406
X-RAY DIFFRACTIONr_bond_other_d0.0010.02975
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9371896
X-RAY DIFFRACTIONr_angle_other_deg0.89132377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71524.54566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.769155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
X-RAY DIFFRACTIONr_nbd_refined0.2160.2263
X-RAY DIFFRACTIONr_nbd_other0.190.2984
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2682
X-RAY DIFFRACTIONr_nbtor_other0.0830.2684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1233877
X-RAY DIFFRACTIONr_mcbond_other0.8883350
X-RAY DIFFRACTIONr_mcangle_it4.39451372
X-RAY DIFFRACTIONr_scbond_it6.768609
X-RAY DIFFRACTIONr_scangle_it8.53211522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 93 -
Rwork0.238 2194 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 16.3155 Å / Origin y: 26.1899 Å / Origin z: 15.5517 Å
111213212223313233
T0.0736 Å20.0082 Å20.0393 Å2--0.2799 Å20.0187 Å2---0.1102 Å2
L1.5707 °20.2649 °2-0.1166 °2-3.4648 °20.5411 °2--2.875 °2
S-0.0068 Å °0.118 Å °0.0225 Å °0.0104 Å °0.1386 Å °0.0535 Å °0.0206 Å °-0.002 Å °-0.1318 Å °

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