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- PDB-6du7: Glutathione reductase from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 6du7
TitleGlutathione reductase from Streptococcus pneumoniae
ComponentsGlutathione reductase
KeywordsOXIDOREDUCTASE / Glutathione reductase / Streptococcus pneumoniae
Function / homology
Function and homology information


glutathione-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Glutathione reductase, eukaryote/bacterial / 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 ...Glutathione reductase, eukaryote/bacterial / 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
FLAVIN-ADENINE DINUCLEOTIDE / THIOCYANATE ION / Glutathione reductase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsMaher, M.J. / Sikanyika, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1080784 Australia
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: The structure and activity of the glutathione reductase from Streptococcus pneumoniae.
Authors: Sikanyika, M. / Aragao, D. / McDevitt, C.A. / Maher, M.J.
History
DepositionJun 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione reductase
B: Glutathione reductase
C: Glutathione reductase
D: Glutathione reductase
E: Glutathione reductase
F: Glutathione reductase
G: Glutathione reductase
H: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,78518
Polymers391,3858
Non-polymers6,40110
Water31,8141766
1
A: Glutathione reductase
F: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4174
Polymers97,8462
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-74 kcal/mol
Surface area35350 Å2
MethodPISA
2
B: Glutathione reductase
C: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4755
Polymers97,8462
Non-polymers1,6293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-78 kcal/mol
Surface area35540 Å2
MethodPISA
3
D: Glutathione reductase
E: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4755
Polymers97,8462
Non-polymers1,6293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-76 kcal/mol
Surface area35520 Å2
MethodPISA
4
G: Glutathione reductase
H: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4174
Polymers97,8462
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-76 kcal/mol
Surface area35250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.748, 172.671, 135.434
Angle α, β, γ (deg.)90.000, 91.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutathione reductase / / Glutathione-disulfide reductase


Mass: 48923.113 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: gor, A5N45_09080, ERS020408_00588, ERS022363_01056 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U0ARX4, glutathione-disulfide reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1766 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris propane, pH 7.0, 0.2 M potassium thiocyanate, 14% PEG3350, 0.1 mM NADP+

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.56→46.6 Å / Num. obs: 141364 / % possible obs: 98.9 % / Redundancy: 3.8 % / Net I/σ(I): 8.7
Reflection shellResolution: 2.56→2.6 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GER

1ger


Resolution: 2.56→46.6 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.236 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.656 / ESU R Free: 0.286 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 7170 5.1 %RANDOM
Rwork0.1799 ---
obs0.1826 134126 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 146.26 Å2 / Biso mean: 43.337 Å2 / Biso min: 4.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å2-0.38 Å2
2---0.81 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.56→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27516 0 430 1766 29712
Biso mean--33.56 36.34 -
Num. residues----3581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01928518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0226883
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.96438619
X-RAY DIFFRACTIONr_angle_other_deg0.843361837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11353571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00623.8221256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96154746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.68915184
X-RAY DIFFRACTIONr_chiral_restr0.0590.24294
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0232229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026515
LS refinement shellResolution: 2.557→2.623 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 434 -
Rwork0.326 8684 -
all-9118 -
obs--86.36 %

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