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- PDB-2j3n: X-ray structure of human thioredoxin reductase 1 -

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Basic information

Entry
Database: PDB / ID: 2j3n
TitleX-ray structure of human thioredoxin reductase 1
ComponentsTHIOREDOXIN REDUCTASE 1
KeywordsOXIDOREDUCTASE / FAD / NADP / HUMAN / SELENIUM / CYTOPLASM / FLAVOPROTEIN / REDOX REGULATION / ELECTRON TRANSPORT / SELENOCYSTEINE / PHOSPHORYLATION / PYRIDINE NUCLEOTIDE DEPENDENT DISULFIDE REDUCTASE / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species / mesoderm formation / FAD binding / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / PPARA activates gene expression / fibrillar center / cellular response to oxidative stress / cell population proliferation / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / 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 ...Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / 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 / Thioredoxin-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase 1, cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFritz-Wolf, K. / Urig, S. / Becker, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Structure of Human Thioredoxin Reductase 1 Provides Insights Into C-Terminal Rearrangements During Catalysis.
Authors: Fritz-Wolf, K. / Urig, S. / Becker, K.
History
DepositionAug 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN REDUCTASE 1
B: THIOREDOXIN REDUCTASE 1
C: THIOREDOXIN REDUCTASE 1
D: THIOREDOXIN REDUCTASE 1
E: THIOREDOXIN REDUCTASE 1
F: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,41623
Polymers341,6516
Non-polymers9,76517
Water79344
1
A: THIOREDOXIN REDUCTASE 1
B: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2969
Polymers113,8842
Non-polymers3,4127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: THIOREDOXIN REDUCTASE 1
D: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0607
Polymers113,8842
Non-polymers3,1765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: THIOREDOXIN REDUCTASE 1
F: THIOREDOXIN REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0607
Polymers113,8842
Non-polymers3,1765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.630, 90.640, 166.600
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
THIOREDOXIN REDUCTASE 1 / TR / TR1


Mass: 56941.867 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLACENTA / Description: CDNA FROM HUMAN PLACENTA USED FOR CLONING / Organ: UTERUS / Plasmid: PET28A / Production host: Escherichia coli M15 (bacteria)
References: UniProt: Q16881, thioredoxin-disulfide reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HISTIDINE TAG AND VECTOR DERIVED SEQUENCE SSGLVPRGSH BEFORE THE ORIGINAL AA SEQUENCE STARTS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 58 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92524
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92524 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 97693 / % possible obs: 92.8 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.35 / % possible all: 79

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6V

1h6v


Resolution: 2.8→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3755560.06 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5
Details: NONCRYSTOLLOGRAPHIC CONSTRAINTS ON ALL MONOMERS EXCEPT SOME REGIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 4562 5 %RANDOM
Rwork0.249 ---
obs0.249 90836 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.4599 Å2 / ksol: 0.307352 e/Å3
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.66 Å20 Å29.19 Å2
2--6.7 Å20 Å2
3---0.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22604 0 646 44 23294
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.372
X-RAY DIFFRACTIONc_scangle_it2.172.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 653 5.1 %
Rwork0.369 12114 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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