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- PDB-7fc2: Crystal Structure of GPX6 -

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Basic information

Entry
Database: PDB / ID: 7fc2
TitleCrystal Structure of GPX6
ComponentsGlutathione peroxidase 6
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / glutathione peroxidase / glutathione peroxidase activity / peroxidase activity / response to oxidative stress / extracellular region
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 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSun, J.
CitationJournal: To Be Published
Title: Crystal Structure of GPX6
Authors: Sun, J.
History
DepositionJul 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Glutathione peroxidase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2144
Polymers24,9261
Non-polymers2883
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.390, 108.922, 120.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Glutathione peroxidase 6 / / GPx-6 / GSHPx-6


Mass: 24926.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpx6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91WR8, glutathione peroxidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.44 Å3/Da / Density % sol: 64.21 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.6 M ammonium sulfate, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44094 / % possible obs: 98.86 % / Redundancy: 9.4 % / Biso Wilson estimate: 24.63 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.048 / Net I/σ(I): 20.17
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 5.94 / Num. unique obs: 2311 / Rpim(I) all: 0.211 / % possible all: 98.84

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R37

2r37


Resolution: 2→30.03 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2075 3744 8.49 %
Rwork0.1886 40350 -
obs0.1902 44094 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.33 Å2
Refinement stepCycle: LAST / Resolution: 2→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 15 185 1756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781660
X-RAY DIFFRACTIONf_angle_d1.03362264
X-RAY DIFFRACTIONf_chiral_restr0.0616233
X-RAY DIFFRACTIONf_plane_restr0.008299
X-RAY DIFFRACTIONf_dihedral_angle_d14.0446215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32071350.24851496X-RAY DIFFRACTION96.34
2.03-2.050.28261400.23871493X-RAY DIFFRACTION98.97
2.05-2.080.24341370.24921502X-RAY DIFFRACTION98.97
2.08-2.110.2611410.25211483X-RAY DIFFRACTION99.02
2.11-2.140.26021390.23871515X-RAY DIFFRACTION99.22
2.14-2.180.28161450.23291519X-RAY DIFFRACTION99.22
2.18-2.210.29461390.22781469X-RAY DIFFRACTION99.14
2.21-2.250.28311420.22731531X-RAY DIFFRACTION99.11
2.25-2.290.2831330.23381514X-RAY DIFFRACTION99.16
2.29-2.330.24141370.22961480X-RAY DIFFRACTION98.9
2.33-2.380.19991470.21821541X-RAY DIFFRACTION99.12
2.38-2.430.2591380.22131493X-RAY DIFFRACTION99.33
2.43-2.490.27971430.21841502X-RAY DIFFRACTION98.68
2.49-2.550.22421330.19991455X-RAY DIFFRACTION98.09
2.55-2.620.1981430.19441555X-RAY DIFFRACTION98.78
2.62-2.70.23041340.20291463X-RAY DIFFRACTION98.4
2.7-2.790.23441380.20641488X-RAY DIFFRACTION98.72
2.79-2.880.19751360.18981520X-RAY DIFFRACTION98.75
2.88-30.19831370.19991481X-RAY DIFFRACTION98.48
3-3.140.20531400.18491510X-RAY DIFFRACTION96.83
3.14-3.30.19611400.18391446X-RAY DIFFRACTION96.3
3.3-3.510.20781420.17641469X-RAY DIFFRACTION96.87
3.51-3.780.15511370.16441482X-RAY DIFFRACTION97.3
3.78-4.160.1851370.14851484X-RAY DIFFRACTION97.71
4.16-4.760.15971320.13761467X-RAY DIFFRACTION96.27
4.76-5.990.15761360.15371499X-RAY DIFFRACTION98.32
5.99-30.030.17071430.17761493X-RAY DIFFRACTION98.14

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