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- PDB-2v6o: Structure of Schistosoma mansoni Thioredoxin-Glutathione Reductas... -

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Basic information

Entry
Database: PDB / ID: 2v6o
TitleStructure of Schistosoma mansoni Thioredoxin-Glutathione Reductase (SmTGR)
ComponentsTHIOREDOXIN GLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / FAD / FLAVOPROTEIN / CHIMERIC ENZYME / THIOL-MEDIATED DETOXIFICATION PATHWAY / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain ...Thioredoxin/glutathione reductase selenoprotein / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / 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 / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NITRATE ION / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMiele, A.E. / Angelucci, F. / Boumis, G. / Dimastrogiovanni, D. / Bellelli, A. / Brunori, M.
CitationJournal: Proteins / Year: 2008
Title: Glutathione Reductase and Thioredoxin Reductase at the Crossroad: The Structure of Schistosoma Mansoni Thioredoxin Glutathione Reductase
Authors: Angelucci, F. / Miele, A.E. / Boumis, G. / Dimastrogiovanni, D. / Brunori, M. / Bellelli, A.
History
DepositionJul 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5257
Polymers64,9011
Non-polymers1,6246
Water5,621312
1
A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules

A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,05114
Polymers129,8022
Non-polymers3,24912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8520 Å2
ΔGint-68.3 kcal/mol
Surface area57430 Å2
MethodPQS
Unit cell
Length a, b, c (Å)142.324, 102.533, 59.027
Angle α, β, γ (deg.)90.00, 112.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIOREDOXIN GLUTATHIONE REDUCTASE


Mass: 64900.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-596
Source method: isolated from a genetically manipulated source
Details: FAD COFACTOR BOUND / Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Description: ADULT CDNA / Plasmid: PGEXT4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q962Y6, EC: 1.6.4.5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBELONGS TO THE CLASS-I PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE FAMILY.
Has protein modificationY
Sequence details2 RESIDUES DELETION 597-598

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.6 %
Description: AFTER FIXING THE FIRST DOMAIN, THE SECOND DOMAIN WAS SEARCHED USING 1Z7R AS STARTING MODEL.
Crystal growpH: 7.2
Details: 22% PEG 3350, 0.1M HEPES PH 7.2, 0.2M NANO3, 5MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 39579 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6V

1h6v


Resolution: 2.2→19.92 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.339 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY FOR RESIDUES 1-7 AND 594-597 WAS NOT VISIBLE, THEREFORE THESE AMINO ACIDS WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1916 5 %RANDOM
Rwork0.188 ---
obs0.191 36440 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.14 Å2
2--0.2 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4492 0 109 312 4913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224809
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0541.9836530
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.9875621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70924.872195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60715820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6481519
X-RAY DIFFRACTIONr_chiral_restr0.1730.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023549
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.22334
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23284
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2381.53095
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81324798
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.97732042
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0734.51717
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 131
Rwork0.206 2618

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