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- PDB-3itj: Crystal structure of Saccharomyces cerevisiae thioredoxin reducta... -

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Basic information

Entry
Database: PDB / ID: 3itj
TitleCrystal structure of Saccharomyces cerevisiae thioredoxin reductase 1 (Trr1)
ComponentsThioredoxin reductase 1
KeywordsOXIDOREDUCTASE / Thioredoxin reductase 1 alpha/beta type protein / Disulfide bond / FAD / Flavoprotein / NADP / Phosphoprotein / Redox-active center
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / ferrous iron binding / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOliveira, M.A. / Discola, K.F. / Alves, S.V. / Medrano, F.J. / Guimaraes, B.G. / Netto, L.E.S.
CitationJournal: Biochemistry / Year: 2010
Title: Insights into the specificity of thioredoxin reductase-thioredoxin interactions. A structural and functional investigation of the yeast thioredoxin system.
Authors: Oliveira, M.A. / Discola, K.F. / Alves, S.V. / Medrano, F.J. / Guimaraes, B.G. / Netto, L.E.
History
DepositionAug 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,56414
Polymers145,2694
Non-polymers4,29510
Water4,990277
1
A: Thioredoxin reductase 1
hetero molecules

D: Thioredoxin reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5906
Polymers72,6342
Non-polymers1,9554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area7570 Å2
ΔGint-30 kcal/mol
Surface area25090 Å2
MethodPISA
2
B: Thioredoxin reductase 1
C: Thioredoxin reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9748
Polymers72,6342
Non-polymers2,3406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-28 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.975, 135.411, 75.819
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-379-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

#1: Protein
Thioredoxin reductase 1 /


Mass: 36317.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W303 / Gene: D9476.5, TRR1, YDR353W / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A
References: UniProt: P29509, thioredoxin-disulfide reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.7 M Sodium citrate pH 4.0, 12% PEG 3000, 0.1 M Trimethylamine hydrochloride. Drop volume of 6.0 ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 5, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.783
11-h,-k,l20.217
ReflectionResolution: 2.4→50 Å / Num. obs: 46488 / % possible obs: 97.03 % / Observed criterion σ(I): 4.3 / Redundancy: 6.1 % / Rsym value: 0.099 / Net I/σ(I): 17.6
Reflection shellResolution: 2.4→2.462 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.32 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VDC

1vdc


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.928 / SU B: 14.808 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19356 2459 5 %RANDOM
Rwork0.1693 ---
obs0.17053 46488 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.636 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å21.94 Å2
2---1.35 Å20 Å2
3---4.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9262 0 290 277 9829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.253213254
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11451251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2824.8350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.859151546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5611538
X-RAY DIFFRACTIONr_chiral_restr0.1410.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217184
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_it0.9931.56217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63829917
X-RAY DIFFRACTIONr_scbond_it2.93833520
X-RAY DIFFRACTIONr_scangle_it4.3264.53336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1967 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.760.5
Bmedium positional0.850.5
Cmedium positional0.720.5
Dmedium positional1.160.5
Amedium thermal1.442
Bmedium thermal1.62
Cmedium thermal1.442
Dmedium thermal1.622
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 220 -
Rwork0.18 3474 -
obs--99.3 %
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)
10.82230.1573-0.16020.7095-0.02170.6633-0.02390.0639-0.0283-0.03080.03610.10730.0599-0.1226-0.01220.04420.0063-0.01140.0482-0.00590.037616.3196-14.146714.9962
20.805-0.1345-0.39561.07530.33011.00220.0011-0.04080.0250.035-0.0047-0.0235-0.02770.01440.00360.0655-0.006300.060.00780.071419.709718.188320.0861
30.9960.2265-0.29861.0321-0.39921.17050.0022-0.055-0.06790.071-0.00270.0390.0562-0.00910.00050.0292-0.0034-0.01290.0461-0.00530.028421.8433-11.650527.1378
41.4877-0.1689-0.37191.71870.31481.24550.03910.04530.1435-0.0128-0.01040.0341-0.1117-0.0708-0.02880.0696-0.0012-0.02350.05560.01540.018728.017269.686814.4603
50.8581-0.0259-0.08120.28320.02380.42670.00740.05530.0633-0.0288-0.0023-0.0189-0.03840.0274-0.00510.0768-0.0051-0.00070.0320.00260.048746.33773.950821.2183
60.7146-0.362-0.26070.99030.42921.2014-0.0029-0.07950.0320.05960.00820.07220.0044-0.0677-0.00540.06410.0015-0.00390.04920.01350.049527.170267.73129.4272
70.8254-0.01360.06830.9789-0.16630.92840.04170.014-0.1492-0.0835-0.00640.03930.1513-0.0051-0.03520.069-0.00440.01210.0693-0.01320.061338.578244.277616.8552
81.13420.0640.01521.2992-0.20670.98520.00160.09520.0055-0.10780.004-0.078-0.01040.0637-0.00550.09410.0009-0.00340.10510.00050.10145.037844.17718.9698
90.9956-0.080.32151.2986-0.27281.32820.0097-0.1249-0.10720.09840.0018-0.02620.05280.0013-0.01140.06070.00710.00990.0486-0.01150.041534.465348.542229.0267
101.02080.12250.47650.24050.00320.7999-0.01120.1064-0.0482-0.0190.0446-0.15490.00320.1594-0.03350.06550.00310.01310.06210.00610.060246.2787132.734914.3973
110.6791-0.38280.36860.93930.00050.6670.00310.02050.0141-0.01890.00180.1128-0.024-0.1226-0.0050.1671-0.00710.00240.1665-0.00150.16843.727398.837718.442
120.94430.36780.33610.46460.14281.0615-0.0027-0.04110.0090.06910.0052-0.04010.00520.016-0.00260.0496-0.00370.01020.06440.00670.046642.3331127.489626.2778
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 123
2X-RAY DIFFRACTION2A124 - 247
3X-RAY DIFFRACTION3A248 - 317
4X-RAY DIFFRACTION4B1 - 65
5X-RAY DIFFRACTION5B66 - 253
6X-RAY DIFFRACTION6B254 - 318
7X-RAY DIFFRACTION7C1 - 122
8X-RAY DIFFRACTION8C123 - 247
9X-RAY DIFFRACTION9C248 - 317
10X-RAY DIFFRACTION10D1 - 122
11X-RAY DIFFRACTION11D123 - 244
12X-RAY DIFFRACTION12D245 - 317

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