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- PDB-3d8x: Crystal Structure of Saccharomyces cerevisiae NDPPH Dependent Thi... -

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Basic information

Entry
Database: PDB / ID: 3d8x
TitleCrystal Structure of Saccharomyces cerevisiae NDPPH Dependent Thioredoxin Reductase 1
ComponentsThioredoxin reductase 1
KeywordsOXIDOREDUCTASE / thioredoxin reductase / NADPH / yeast / ModPipe Model of A6Z / FAD / Flavoprotein / 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-NDP / Thioredoxin reductase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, Z.Y. / Bao, R. / Yu, J. / Chen, Y.X. / Zhou, C.-Z.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Crystal structure of Saccharomyces cerevisiae cytoplasmic thioredoxin reductase Trr1 reveals the structural basis for species-specific recognition of thioredoxin
Authors: Zhang, Z. / Bao, R. / Zhang, Y. / Yu, J. / Zhou, C.-Z. / Chen, Y.
History
DepositionMay 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Nov 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6425
Polymers70,3262
Non-polymers2,3173
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-36 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.229, 125.004, 60.967
Angle α, β, γ (deg.)90.00, 114.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin reductase 1 /


Mass: 35162.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: TRR1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P29509, thioredoxin-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5 / Details: pH 6.5, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 20419 / Num. obs: 19676 / % possible obs: 93.4 % / Observed criterion σ(F): 6 / Redundancy: 3 % / Biso Wilson estimate: 56.9 Å2 / Rsym value: 0.15 / Net I/σ(I): 4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 1938 / Rsym value: 0.47 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
AUTOMARdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VDC

1vdc


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.462 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23431 912 5.2 %RANDOM
Rwork0.22581 ---
obs0.22625 16736 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.656 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å23.25 Å2
2---0.31 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 130 100 5016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2232.0036793
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.5055634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77225.08187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.05215850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4191519
X-RAY DIFFRACTIONr_chiral_restr0.0890.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023652
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.22266
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23427
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.227
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_it0.471.53209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73225048
X-RAY DIFFRACTIONr_scbond_it0.88532098
X-RAY DIFFRACTIONr_scangle_it1.4484.51745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 66 -
Rwork0.312 1225 -
obs--95.77 %
Refinement TLS params.Method: refined / Origin x: -2.289 Å / Origin y: -9.285 Å / Origin z: 30.071 Å
111213212223313233
T-0.1683 Å20.0434 Å2-0.0464 Å2--0.0006 Å20.0616 Å2---0.1854 Å2
L1.3929 °2-0.4551 °2-0.103 °2-1.5487 °20.1914 °2--2.2233 °2
S-0.1471 Å °-0.2375 Å °-0.1084 Å °0.1264 Å °0.1194 Å °0.0939 Å °-0.0432 Å °-0.0264 Å °0.0277 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 12110 - 128
2X-RAY DIFFRACTION1AA251 - 318258 - 325

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