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- PDB-1gp1: THE REFINED STRUCTURE OF THE SELENOENZYME GLUTATHIONE PEROXIDASE ... -

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Basic information

Entry
Database: PDB / ID: 1gp1
TitleTHE REFINED STRUCTURE OF THE SELENOENZYME GLUTATHIONE PEROXIDASE AT 0.2-NM RESOLUTION
ComponentsGLUTATHIONE PEROXIDASE
KeywordsOXIDOREDUCTASE(H2O2(A))
Function / homology
Function and homology information


Synthesis of 12-eicosatetraenoic acid derivatives / positive regulation of supramolecular fiber organization / endothelial cell development / phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / response to symbiotic bacterium / regulation of mammary gland epithelial cell proliferation / glutathione peroxidase / Detoxification of Reactive Oxygen Species / lipoxygenase pathway ...Synthesis of 12-eicosatetraenoic acid derivatives / positive regulation of supramolecular fiber organization / endothelial cell development / phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / response to symbiotic bacterium / regulation of mammary gland epithelial cell proliferation / glutathione peroxidase / Detoxification of Reactive Oxygen Species / lipoxygenase pathway / blood vessel endothelial cell migration / Lewy body / arachidonate metabolic process / response to selenium ion / skeletal muscle tissue regeneration / glutathione peroxidase activity / UV protection / myoblast differentiation / angiogenesis involved in wound healing / response to hydroperoxide / biological process involved in interaction with symbiont / intrinsic apoptotic signaling pathway in response to oxidative stress / triglyceride metabolic process / temperature homeostasis / heart contraction / negative regulation of release of cytochrome c from mitochondria / fat cell differentiation / myoblast proliferation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / skeletal muscle fiber development / regulation of proteasomal protein catabolic process / glutathione metabolic process / cell redox homeostasis / protein tyrosine kinase binding / epigenetic regulation of gene expression / response to gamma radiation / hydrogen peroxide catabolic process / negative regulation of inflammatory response to antigenic stimulus / response to hydrogen peroxide / sensory perception of sound / SH3 domain binding / vasodilation / cellular response to oxidative stress / fibroblast proliferation / neuron apoptotic process / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to xenobiotic stimulus / mitochondrion / 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
Glutathione peroxidase 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEpp, O. / Ladenstein, R.
Citation
Journal: Eur.J.Biochem. / Year: 1983
Title: The refined structure of the selenoenzyme glutathione peroxidase at 0.2-nm resolution.
Authors: Epp, O. / Ladenstein, R. / Wendel, A.
#1: Journal: J.Mol.Biol. / Year: 1979
Title: Structure Analysis and Molecular Model of the Selenoenzyme Glutathione Peroxidase at 2.8 Angstroms Resolution
Authors: Ladenstein, R. / Epp, O. / Bartels, K. / Jones, A. / Huber, R. / Wendel, A.
#2: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1984
Title: The Amino-Acid Sequence of Bovine Glutathione Peroxidase
Authors: Guenzler, W.A. / Steffens, G.J. / Grossmann, A. / Kim, S.-M.A. / Oetting, F. / Wendel, A. / Flohe, L.
History
DepositionJun 11, 1985Processing site: BNL
Revision 1.0Nov 8, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 25, 2013Group: Non-polymer description
Revision 2.0Nov 29, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site
Revision 3.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_peptide_omega.omega / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_symm_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[3] / _struct_ref_seq_dif.details
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE PEROXIDASE
B: GLUTATHIONE PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)43,9322
Polymers43,9322
Non-polymers00
Water3,333185
1
A: GLUTATHIONE PEROXIDASE
B: GLUTATHIONE PEROXIDASE

A: GLUTATHIONE PEROXIDASE
B: GLUTATHIONE PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)87,8644
Polymers87,8644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)90.400, 109.500, 58.200
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: SEE REMARK 7. / 2: RESIDUES 97 AND 150 OF EACH CHAIN ARE CIS PROLINES. / 3: SEE REMARK 6.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.131858, -0.010348, 0.991227), (0.00237, -0.99994, -0.010752), (0.991204, 0.003773, -0.131818)
Vector: -25.02745, 75.56879, 29.04819)

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Components

#1: Protein GLUTATHIONE PEROXIDASE


Mass: 21965.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: ERYTHROCYTE / References: UniProt: P00435, glutathione peroxidase
#2: Water ChemComp-HOH / 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

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal grow
*PLUS
pH: 7.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mM11H2O2
25 mMphosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 26564 / % possible obs: 71 % / Num. measured all: 93223 / Rmerge(I) obs: 0.101

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2→6 Å / Rfactor Rwork: 0.171
Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP.
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 0 185 3111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.1
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it0.23
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Num. reflection obs: 24798 / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS

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