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- PDB-3eao: Crystal structure of recombinant rat selenoprotein thioredoxin re... -

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Basic information

Entry
Database: PDB / ID: 3eao
TitleCrystal structure of recombinant rat selenoprotein thioredoxin reductase 1 with oxidized C-terminal tail
ComponentsThioredoxin reductase 1, cytoplasmic
KeywordsOXIDOREDUCTASE / Selenoprotein / mammalian thioredoxin reductase 1 / selenocysteine / selenenylsulfide / FAD / Flavoprotein / NADP / Phosphoprotein / Redox-active center / Selenium
Function / homology
Function and homology information


selenate reductase activity / halogen metabolic process / Metabolism of ingested MeSeO2H into MeSeH / benzene-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / selenocysteine metabolic process / Detoxification of Reactive Oxygen Species / NADPH peroxidase / NADPH peroxidase activity / cellular response to hyperoxia ...selenate reductase activity / halogen metabolic process / Metabolism of ingested MeSeO2H into MeSeH / benzene-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / selenocysteine metabolic process / Detoxification of Reactive Oxygen Species / NADPH peroxidase / NADPH peroxidase activity / cellular response to hyperoxia / TP53 Regulates Metabolic Genes / NADPH oxidation / mercury ion binding / NAD(P)H oxidase H2O2-forming activity / thioredoxin-disulfide reductase / response to selenium ion / thioredoxin-disulfide reductase (NADPH) activity / mesoderm formation / gastrulation / response to axon injury / response to hyperoxia / cellular response to copper ion / FAD binding / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cell population proliferation / response to xenobiotic stimulus / positive regulation of apoptotic process / neuronal cell body / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / 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 ...Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase 1, cytoplasmic
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSandalova, T. / Cheng, Q. / Lindqvist, Y. / Arner, E.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Crystal structure and catalysis of the selenoprotein thioredoxin reductase 1.
Authors: Cheng, Q. / Sandalova, T. / Lindqvist, Y. / Arner, E.S.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: High-level expression in Escherichia coli of selenocysteine-containing rat thioredoxin reductase utilizing gene fusions with engineered bacterial-type SECIS elements and co-expression with the ...Title: High-level expression in Escherichia coli of selenocysteine-containing rat thioredoxin reductase utilizing gene fusions with engineered bacterial-type SECIS elements and co-expression with the selA, selB and selC genes.
Authors: Arner, E.S. / Sarioglu, H. / Lottspeich, F. / Holmgren, A. / Bock, A.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 29, 2012Group: Derived calculations
Revision 1.3Feb 19, 2014Group: Atomic model / Database references / Structure summary
Revision 1.4Aug 6, 2014Group: Derived calculations / Structure summary
Revision 1.5Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Aug 30, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase 1, cytoplasmic
B: Thioredoxin reductase 1, cytoplasmic
C: Thioredoxin reductase 1, cytoplasmic
D: Thioredoxin reductase 1, cytoplasmic
E: Thioredoxin reductase 1, cytoplasmic
F: Thioredoxin reductase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,59118
Polymers328,4186
Non-polymers9,17412
Water64936
1
A: Thioredoxin reductase 1, cytoplasmic
B: Thioredoxin reductase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5306
Polymers109,4732
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-88 kcal/mol
Surface area36780 Å2
MethodPISA
2
C: Thioredoxin reductase 1, cytoplasmic
D: Thioredoxin reductase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5306
Polymers109,4732
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-89 kcal/mol
Surface area36820 Å2
MethodPISA
3
E: Thioredoxin reductase 1, cytoplasmic
F: Thioredoxin reductase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5306
Polymers109,4732
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-91 kcal/mol
Surface area36560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.231, 137.754, 168.954
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A10 - 113
2111B10 - 113
3111C10 - 113
4111D10 - 113
5111E10 - 113
6111F10 - 113
1211A115 - 492
2211B115 - 492
3211C115 - 492
4211D115 - 492
5211E115 - 492
6211F115 - 492
1311A600 - 601
2311B600 - 601
3311C600 - 601
4311D600 - 601
5311E600 - 601
6311F600 - 601
1121A493 - 499
2121B493 - 499
3121C493 - 499
4121D493 - 499
5121E493 - 499
6121F493 - 499

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a dimer, the unit cell contains three dimers

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Components

#1: Protein
Thioredoxin reductase 1, cytoplasmic / / TR / Thioredoxin reductase TR1 / NADPH-dependent thioredoxin reductase


Mass: 54736.293 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: residue 426 is Ile / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley / Gene: Txnrd1, Trxr1 / Plasmid: pTRSter / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O89049, thioredoxin-disulfide reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE MATCHES WITH NP_113802 FROM NCBI DATABASE

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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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, PEG 3350 15%, 12% of ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.908 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2007 / Details: mirrors
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 3.1→64 Å / Num. all: 64804 / Num. obs: 64804 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 10.9
Reflection shellResolution: 3.101→3.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EAN

3ean


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.83 / SU B: 26.935 / SU ML: 0.46 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28873 3276 5.1 %RANDOM
Rwork0.2564 ---
all0.25806 61139 --
obs0.25806 61139 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.314 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.25 Å2
2--0.07 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22568 0 510 36 23114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02223561
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.99531993
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83752930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85224.754957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.532154013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.97815102
X-RAY DIFFRACTIONr_chiral_restr0.0980.23596
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217455
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.211663
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.216017
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2777
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3840.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4921.514832
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.839223320
X-RAY DIFFRACTIONr_scbond_it1.017310005
X-RAY DIFFRACTIONr_scangle_it1.7244.58673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3755tight positional0.050.05
12B3755tight positional0.050.05
13C3755tight positional0.060.05
14D3755tight positional0.050.05
15E3755tight positional0.050.05
16F3755tight positional0.060.05
21A44tight positional0.070.05
22B44tight positional0.10.05
23C44tight positional0.20.05
24D44tight positional0.10.05
25E44tight positional0.080.05
26F44tight positional0.080.05
11A3755tight thermal0.080.5
12B3755tight thermal0.080.5
13C3755tight thermal0.090.5
14D3755tight thermal0.110.5
15E3755tight thermal0.110.5
16F3755tight thermal0.130.5
21A44tight thermal0.060.5
22B44tight thermal0.050.5
23C44tight thermal0.050.5
24D44tight thermal0.060.5
25E44tight thermal0.050.5
26F44tight thermal0.060.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 247 -
Rwork0.34 4475 -
obs--99.85 %

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