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- PDB-3dk4: Catalytic cycle of human glutathione reductase near 1 A resolution -

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Basic information

Entry
Database: PDB / ID: 3dk4
TitleCatalytic cycle of human glutathione reductase near 1 A resolution
ComponentsGlutathione reductase
KeywordsOXIDOREDUCTASE / flavoenzyme / glutathione / nicotinamide / Alternative initiation / FAD / Flavoprotein / Mitochondrion / NADP / Phosphoprotein / Redox-active center / Transit peptide
Function / homology
Function and homology information


glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / flavin adenine dinucleotide binding ...glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / flavin adenine dinucleotide binding / NADP binding / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / external side of plasma membrane / mitochondrion / extracellular exosome / cytosol
Similarity search - Function
Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily ...Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / GLUTATHIONE / Chem-NDP / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsBerkholz, D.S. / Faber, H.R. / Savvides, S.N. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Catalytic cycle of human glutathione reductase near 1 A resolution.
Authors: Berkholz, D.S. / Faber, H.R. / Savvides, S.N. / Karplus, P.A.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2013Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8786
Polymers51,6361
Non-polymers2,2425
Water16,069892
1
A: Glutathione reductase
hetero molecules

A: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,75612
Polymers103,2722
Non-polymers4,48310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15290 Å2
ΔGint-118 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.031, 62.281, 83.980
Angle α, β, γ (deg.)90.00, 121.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-79-

MET

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutathione reductase / GRase / GR


Mass: 51636.242 Da / Num. of mol.: 1 / Fragment: UNP residues 45 to 522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSR, GLUR, GRD1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00390, glutathione-disulfide reductase

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Non-polymers , 5 types, 897 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 298 K / pH: 7
Details: 3% ammonium sulfate, 0.1 M potassium phosphate and 0.1% beta-octyl glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 192443 / % possible obs: 91 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.4
Reflection shellResolution: 1.1→1.12 Å / Rmerge(I) obs: 0.33 / % possible all: 74.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT3.006data extraction
CNSphasing
SHELXL-97refinement
RefinementStarting model: PDB ENTRY 3DK9

3dk9


Resolution: 1.2→50 Å / Occupancy max: 1 / Occupancy min: 0.11 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.164 7671 4.9 %RANDOM
obs0.114 -91 %-
all-155146 --
Displacement parametersBiso mean: 25.332 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 146 892 4534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0289
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.101

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