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- PDB-3sqp: Structure of human glutathione reductase complexed with pyocyanin... -

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Basic information

Entry
Database: PDB / ID: 3sqp
TitleStructure of human glutathione reductase complexed with pyocyanin, an agent with antimalarial activity
ComponentsGlutathione reductase, mitochondrial
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / CELLULAR REDUCTANTS / GLUTATHIONE REDUCTASE / PLASMODIUM FALCIPARUM / PYOCYANIN / ALTERNATIVE INITIATION / FLAVOPROTEIN / MITOCHONDRION / OXIDOREDUCTASE / PHOSPHOPROTEIN / REDOX-ACTIVE CENTER / TRANSIT PEPTIDE / OXIDOREDUCTASE-ANTIBIOTIC complex
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
5-methylphenazin-1(5H)-one / FLAVIN-ADENINE DINUCLEOTIDE / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsFritz-Wolf, K. / Schirmer, R.H. / Koenig, I. / Goebel, U.
CitationJournal: Redox Rep. / Year: 2011
Title: The bacterial redox signaller pyocyanin as an antiplasmodial agent: comparisons with its thioanalog methylene blue.
Authors: Kasozi, D.M. / Gromer, S. / Adler, H. / Zocher, K. / Rahlfs, S. / Wittlin, S. / Fritz-Wolf, K. / Schirmer, R.H. / Becker, K.
History
DepositionJul 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)105,83212
Polymers103,2722
Non-polymers2,56010
Water15,169842
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-50 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.080, 67.370, 78.860
Angle α, β, γ (deg.)68.98, 66.81, 62.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 18:478 ) and (not element H)
211chain B and (resseq 18:478 ) and (not element H)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione reductase, mitochondrial / GR / GRase


Mass: 51636.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P00390, glutathione-disulfide reductase

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Non-polymers , 5 types, 852 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-3J8 / 5-methylphenazin-1(5H)-one / Pyocyanin / Pyrocyanine / Sanasin / Sanazin


Mass: 210.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10N2O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 842 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growpH: 7.5
Details: 660 MM AMMONIUM SULFATE, 100 MM POTASSIUM PHOSPHATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 27, 2008 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→37.71 Å / Num. obs: 47828 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Rsym value: 0.029
Reflection shellResolution: 2.21→2.25 Å / % possible all: 78

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DJJ
Resolution: 2.21→37.71 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 2870 6 %
Rwork0.144 --
obs0.146 47819 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.5 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 22.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.903 Å21.98 Å20.005 Å2
2---1.5 Å21.871 Å2
3---0.597 Å2
Refinement stepCycle: LAST / Resolution: 2.21→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 170 842 8010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057335
X-RAY DIFFRACTIONf_angle_d0.9039958
X-RAY DIFFRACTIONf_dihedral_angle_d16.3062688
X-RAY DIFFRACTIONf_chiral_restr0.0581116
X-RAY DIFFRACTIONf_plane_restr0.0051240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3500X-RAY DIFFRACTIONPOSITIONAL
12B3500X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.212-2.250.1941210.1411893X-RAY DIFFRACTION78
2.25-2.2910.1991380.1442165X-RAY DIFFRACTION93
2.291-2.3360.1951420.142229X-RAY DIFFRACTION93
2.336-2.3830.2091440.1462255X-RAY DIFFRACTION93
2.383-2.4350.1941400.142185X-RAY DIFFRACTION93
2.435-2.4920.2041450.142280X-RAY DIFFRACTION94
2.492-2.5540.1761430.1372233X-RAY DIFFRACTION94
2.554-2.6230.191430.142242X-RAY DIFFRACTION94
2.623-2.70.1891450.1372274X-RAY DIFFRACTION95
2.7-2.7870.1831430.1392249X-RAY DIFFRACTION95
2.787-2.8870.1921450.1432267X-RAY DIFFRACTION95
2.887-3.0020.1811440.142254X-RAY DIFFRACTION95
3.002-3.1390.1651460.1352287X-RAY DIFFRACTION95
3.139-3.3040.1881450.1392278X-RAY DIFFRACTION96
3.304-3.5110.1611470.1362300X-RAY DIFFRACTION96
3.511-3.7820.1721470.1322307X-RAY DIFFRACTION96
3.782-4.1620.1711490.1282326X-RAY DIFFRACTION96
4.162-4.7640.1441460.122287X-RAY DIFFRACTION97
4.764-5.9980.1681470.1562310X-RAY DIFFRACTION97
5.998-37.7150.1931500.1732328X-RAY DIFFRACTION97

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