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- PDB-2gh5: Crystal Structure of human Glutathione Reductase complexed with a... -

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Basic information

Entry
Database: PDB / ID: 2gh5
TitleCrystal Structure of human Glutathione Reductase complexed with a Fluoro-Analogue of the Menadione Derivative M5
Componentsglutathione reductase, mitochondrial
KeywordsOXIDOREDUCTASE / human glutathione reductase / A Fluoro-Analogue of the Menadione Derivative M5
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 / NADP 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 / NADP binding / flavin adenine dinucleotide 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 / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / 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 / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / 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
Chem-ELI / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFritz-Wolf, K. / Winzer, A. / Bauer, H. / Schirmer, H. / Davioud-Charvet, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: A fluoro analogue of the menadione derivative 6-[2'-(3'-methyl)-1',4'-naphthoquinolyl]hexanoic acid is a suicide substrate of glutathione reductase. Crystal structure of the alkylated human enzyme
Authors: Bauer, H. / Fritz-Wolf, K. / Winzer, A. / Little, S. / Yardley, V. / Vezin, H. / Palfey, B. / Schirmer, R.H. / Davioud-Charvet, E.
History
DepositionMar 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 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

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Assembly

Deposited unit
A: glutathione reductase, mitochondrial
B: glutathione reductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,90122
Polymers103,2722
Non-polymers3,62920
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-100 kcal/mol
Surface area37070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.700, 63.600, 103.990
Angle α, β, γ (deg.)90.00, 101.12, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. The the asymmetric unit contains a dimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein glutathione reductase, mitochondrial / E.C.1.8.1.7 / GR / GRase


Mass: 51636.242 Da / Num. of mol.: 2 / Fragment: glutathione reductase
Source method: isolated from a genetically manipulated source
Details: alkylation of CYS 58 by ELI is formed by fluoro-ELI, see REMARK 600
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, 723 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ELI / 6-(3-METHYL-1,4-DIOXO-1,4-DIHYDRONAPHTHALEN-2-YL)HEXANOIC ACID


Mass: 286.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18O4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM potassium phosphate, pH 8.0 and 16% NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2004
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 119525 / Num. obs: 118141 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.052 / Net I/σ(I): 17
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.4 / Num. unique all: 9686 / Rsym value: 0.31 / % possible all: 98.2

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Processing

Software
NameClassification
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GRA

1gra


Resolution: 1.7→19.74 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1963809.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5908 5 %RANDOM
Rwork0.224 ---
all0.2241 119304 --
obs0.2241 118140 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.3232 Å2 / ksol: 0.409971 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å20 Å22.87 Å2
2---0.51 Å20 Å2
3---4.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 240 703 7941
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 972 5 %
Rwork0.276 18460 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramfad-nap-eli-gol
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fad-nap-eli-golwater.top

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