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- PDB-2x99: Thioredoxin glutathione reductase from Schistosoma mansoni in com... -

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Basic information

Entry
Database: PDB / ID: 2x99
TitleThioredoxin glutathione reductase from Schistosoma mansoni in complex with NADPH
ComponentsTHIOREDOXIN GLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / THIOREDOXIN / GLUTATHIONE / NADPH / DETOXIFICATION PATHWAY
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / flavin adenine dinucleotide binding / metal ion binding
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 / GLUTATHIONE / Chem-NDP / DI(HYDROXYETHYL)ETHER / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsAngelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Mapping the Catalytic Cycle of Schistosoma Mansoni Thioredoxin Glutathione Reductase by X-Ray Crystallography
Authors: Angelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A.
#1: Journal: 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.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: Inhibition of Schistosoma Mansoni Thioredoxin- Glutathione Reductase by Auranofin: Structural and Kinetic Aspects.
Authors: Angelucci, F. / Sayed, A.A. / Williams, D.L. / Boumis, G. / Brunori, M. / Dimastrogiovanni, D. / Miele, A.E. / Pauly, F. / Bellelli, A.
History
DepositionMar 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Jul 12, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,85517
Polymers65,0611
Non-polymers3,79416
Water3,333185
1
A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules

A: THIOREDOXIN GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,70934
Polymers130,1222
Non-polymers7,58732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area23260 Å2
ΔGint-37.7 kcal/mol
Surface area45690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.502, 102.610, 59.938
Angle α, β, γ (deg.)90.00, 112.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THIOREDOXIN GLUTATHIONE REDUCTASE


Mass: 65061.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q962Y6, EC: 1.6.4.5

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Non-polymers , 7 types, 201 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


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


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 597 IS GIVEN AS X IN UNIPROT, IT IS CYS IN THIS CONSTRUCT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.16 % / Description: 2V6O USED AS STARTING MODEL
Crystal growpH: 7.4
Details: 0.1 M HEPES AT PH 7.0, 20% PEG 3350, 0.2 M KSCN, 5 MM GSH, 0.4 MM NADPH.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 33294 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
PDBSETphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.246 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. RESIDUES 1-5 AND 593-598 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. RESIDUES 1-5 AND 593-598 OF CHAIN A ARE NOT VISIBLE BY THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.23119 1743 5 %RANDOM
Rwork0.18971 ---
obs0.19176 33294 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.527 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å2-0.58 Å2
2---3.33 Å20 Å2
3---4.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 249 185 4930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224837
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3022.0116526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22824.865185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3751517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213485
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5161.52906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98724688
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.62531931
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6784.51836
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 120 -
Rwork0.219 2440 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.46390.5867-2.77782.6999-0.43784.2689-0.20470.32890.3671-0.32180.18380.4253-0.12580.05320.02090.1057-0.0823-0.05230.0760.04260.238132.10829.86-5.309
21.66741.8237-0.92122.244-1.42241.2381-0.0419-0.00150.0908-0.1002-0.01490.06490.06230.05280.05670.1031-0.02010.01430.0587-0.0280.172238.6624.970.724
31.97280.25831.11860.4135-0.1330.8831-0.0056-0.1049-0.0314-0.06120.03710.03350.0474-0.0476-0.03150.11130.0294-0.00520.0793-0.02120.145512.029-10.028.489
41.20351.2242-0.68781.4656-0.88860.9332-0.0149-0.1152-0.01810.0121-0.0114-0.12180.07530.13620.02630.07660.0474-0.02050.1341-0.05450.145129.392.80118.572
51.4891-1.04020.53861.7758-1.13311.0412-0.1072-0.20880.07310.01170.0796-0.06910.0336-0.08440.02750.09880.04140.00240.1109-0.0180.07973.76-8.97626.298
60.82050.6061-0.17740.78980.00940.1860.0573-0.09860.19490.0957-0.01170.0935-0.00150.0447-0.04560.09080.007-0.01750.076-0.06790.167218.93814.50117.647
70.71150.19950.07921.0307-0.07340.9721-0.0159-0.06610.1279-0.00240.06210.0627-0.0239-0.087-0.04620.06980.0341-0.00390.0396-0.00740.189-7.2912.769.855
81.1531-0.5482-1.40461.1323-0.09814.2135-0.02580.0461-0.05140.0091-0.05020.3710.0341-0.10690.07610.0714-0.0255-0.00740.06220.00180.3052-13.94311.6554.035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 58
2X-RAY DIFFRACTION2A59 - 136
3X-RAY DIFFRACTION3A137 - 211
4X-RAY DIFFRACTION4A212 - 284
5X-RAY DIFFRACTION5A285 - 385
6X-RAY DIFFRACTION6A386 - 478
7X-RAY DIFFRACTION7A479 - 565
8X-RAY DIFFRACTION8A566 - 592

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