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- PDB-1zdl: Crystal Structure of Mouse Thioredoxin Reductase Type 2 -

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Basic information

Entry
Database: PDB / ID: 1zdl
TitleCrystal Structure of Mouse Thioredoxin Reductase Type 2
ComponentsThioredoxin reductase 2, mitochondrial
KeywordsOXIDOREDUCTASE / Selenocysteine / thioredoxin / reductase / flavoprotein
Function / homology
Function and homology information


response to oxygen radical / Detoxification of Reactive Oxygen Species / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / hemopoiesis / cell redox homeostasis / flavin adenine dinucleotide binding / heart development / protein homodimerization activity / mitochondrion
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / 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 ...Thioredoxin/glutathione reductase selenoprotein / : / 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 / Chem-NDP / Thioredoxin reductase 2, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBiterova, E.I. / Turanov, A.A. / Gladyshev, V.N. / Barycki, J.J.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structures of oxidized and reduced mitochondrial thioredoxin reductase provide molecular details of the reaction mechanism.
Authors: Biterova, E.I. / Turanov, A.A. / Gladyshev, V.N. / Barycki, J.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Three-dimensional structure of a mammalian thioredoxin reductase: Implications for mechanism and evolution of a selenocysteine-dependent enzyme.
Authors: Sandalova, T. / Zhong, L. / Lindqvist, Y. / Holmgren, A. / Schneider, G.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Refined structure of glutathione reductase at 1.54 A resolution.
Authors: Karplus, P.A. / Schulz, G.E.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3483
Polymers55,8171
Non-polymers1,5312
Water28816
1
A: Thioredoxin reductase 2, mitochondrial
hetero molecules

A: Thioredoxin reductase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6956
Polymers111,6332
Non-polymers3,0624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
Buried area13050 Å2
ΔGint-79 kcal/mol
Surface area36340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.070, 109.070, 204.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Thioredoxin reductase 2, mitochondrial / TR3


Mass: 55816.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Txnrd2, Trxr2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: Q9JLT4, thioredoxin-disulfide reductase (NADPH)
#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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES, 24% Peg 550 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→32.68 Å / Num. all: 12754 / Num. obs: 12754 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.29 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 17.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 16.66 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
CNS1.1refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H6V

1h6v


Resolution: 3→32.69 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 182218.3 / 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
Rfree0.31 1255 9.8 %RANDOM
Rwork0.241 ---
obs0.241 12754 99.9 %-
all-12754 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.2389 Å2 / ksol: 0.289304 e/Å3
Displacement parametersBiso mean: 61.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å20 Å2
2--3.24 Å20 Å2
3----6.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 101 16 3805
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0
X-RAY DIFFRACTIONc_mcangle_it0
X-RAY DIFFRACTIONc_scbond_it0
X-RAY DIFFRACTIONc_scangle_it0
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 193 9.3 %
Rwork0.323 1888 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2fad.topfad.par
X-RAY DIFFRACTION3ndp.topndp.par
X-RAY DIFFRACTION4water_rep.topwater_rep.param

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