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- PDB-4up3: Crystal structure of the mutant C140S,C286Q thioredoxin reductase... -

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Basic information

Entry
Database: PDB / ID: 4up3
TitleCrystal structure of the mutant C140S,C286Q thioredoxin reductase from Entamoeba histolytica
ComponentsTHIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / REDOX METABOLISM / OXIDATIVE STRESS
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / nucleotide binding / cytosol
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / 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
Similarity search - Component
Biological speciesENTAMOEBA HISTOLYTICA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsPodust, L.M. / Vieira, D.F.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: X-Ray Structures of Thioredoxin and Thioredoxin Reductase from Entamoeba Histolytica and Prevailing Hypothesis of the Mechanism of Auranofin Action.
Authors: Parsonage, D. / Sheng, F. / Hirata, K. / Debnath, A. / Mckerrow, J.H. / Reed, S.L. / Abagyan, R. / Poole, L.B. / Podust, L.M.
History
DepositionJun 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN REDUCTASE
B: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7017
Polymers67,5772
Non-polymers3,1245
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-34.2 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.775, 92.048, 102.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOREDOXIN REDUCTASE


Mass: 33788.523 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTAMOEBA HISTOLYTICA (eukaryote) / Plasmid: PTRCHISA / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834
References: UniProt: C4LW95, thioredoxin-disulfide reductase
#2: Chemical ChemComp-FAD / 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


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIT IS A RECOMBINANT CONSTRUCTION OF THE MUTANT C140S, C286Q OF THIOREDOXIN REDUCTASE OF ENTAMOEBA HISTOLYTICA

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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: 2.31 Å3/Da / Density % sol: 46.83 % / Description: NONE
Crystal growpH: 7.9
Details: 0.2M LITHIUM ACETATE DIHYDRATE, 20% PEG 3350, PH 7.9

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESERCH / Detector: CCD / Date: May 4, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.44→102.94 Å / Num. obs: 91837 / % possible obs: 81.2 % / Observed criterion σ(I): 0.5 / Redundancy: 3.7 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 1.44→1.52 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.3 / % possible all: 36.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A65

4a65


Resolution: 1.44→68.62 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.907 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18073 4584 5 %RANDOM
Rwork0.12596 ---
obs0.12866 87129 80.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.44→68.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 206 767 5675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195166
X-RAY DIFFRACTIONr_bond_other_d0.0020.024817
X-RAY DIFFRACTIONr_angle_refined_deg2.0322.0137055
X-RAY DIFFRACTIONr_angle_other_deg0.946311107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9624.646198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51115824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1521520
X-RAY DIFFRACTIONr_chiral_restr0.1230.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021143
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_it2.5332.1092546
X-RAY DIFFRACTIONr_mcbond_other2.5192.1082545
X-RAY DIFFRACTIONr_mcangle_it2.83.1663197
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1552.5852620
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.97839983
X-RAY DIFFRACTIONr_sphericity_free22.6445212
X-RAY DIFFRACTIONr_sphericity_bonded9.99610423
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 146 -
Rwork0.405 2416 -
obs--30.89 %

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