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- PDB-5m5j: Thioredoxin reductase from Giardia duodenalis -

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Basic information

Entry
Database: PDB / ID: 5m5j
TitleThioredoxin reductase from Giardia duodenalis
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / reductase / flavoprotein
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / nucleotide binding / cytoplasm
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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFiorillo, A. / Ilari, A. / Lalle, M.
CitationJournal: Eur J Med Chem / Year: 2017
Title: Structural characterization of Giardia duodenalis thioredoxin reductase (gTrxR) and computational analysis of its interaction with NBDHEX.
Authors: Brogi, S. / Fiorillo, A. / Chemi, G. / Butini, S. / Lalle, M. / Ilari, A. / Gemma, S. / Campiani, G.
History
DepositionOct 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)71,9685
Polymers70,3742
Non-polymers1,5943
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.643, 85.643, 163.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSALAALA6AA123 - 240134 - 251
211CYSCYSALAALA6BB123 - 240134 - 251
112GLYGLYLEULEU5AA10 - 11021 - 121
212GLYGLYLEULEU5BB10 - 11021 - 121
122ARGARGLEULEU5AA230 - 310241 - 321
222ARGARGLEULEU5BB230 - 310241 - 321

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.567559, -0.293163, -0.769371), (0.338032, -0.935041, 0.106927), (-0.750741, -0.199384, 0.629789)-63.20219, 21.94482, -24.95962

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Components

#1: Protein Thioredoxin reductase


Mass: 35186.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Gene: GL50803_9827 / Production host: Escherichia coli (E. coli)
References: UniProt: E2RU27, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BIS-TRIS hydrochloride 0.1 M pH 6.5, PEG 5000 MME 20% w/V

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.65→48.6 Å / Num. obs: 18404 / % possible obs: 99.8 % / Observed criterion σ(F): 6 / Redundancy: 16 % / CC1/2: 0.994 / Rmerge(I) obs: 0.262 / Net I/σ(I): 12.1
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 15.3 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.767 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d8x

3d8x


Resolution: 2.65→48.6 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.432 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26001 956 5.2 %RANDOM
Rwork0.20177 ---
obs0.20483 17391 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.757 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---1.75 Å20 Å2
3---3.5 Å2
Refinement stepCycle: 1 / Resolution: 2.65→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 107 39 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194801
X-RAY DIFFRACTIONr_bond_other_d0.0020.024492
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9746525
X-RAY DIFFRACTIONr_angle_other_deg0.888310322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10224.521188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46815773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.641523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021039
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_it1.714.5712486
X-RAY DIFFRACTIONr_mcbond_other1.7084.5712485
X-RAY DIFFRACTIONr_mcangle_it2.9226.8523105
X-RAY DIFFRACTIONr_mcangle_other2.9216.8523106
X-RAY DIFFRACTIONr_scbond_it1.5164.5722315
X-RAY DIFFRACTIONr_scbond_other1.5164.5722316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6216.793419
X-RAY DIFFRACTIONr_long_range_B_refined4.73335.0935195
X-RAY DIFFRACTIONr_long_range_B_other4.73335.0935195
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
221064medium positional10.5
111578loose positional0.695
221568loose positional1.335
221064medium thermal7.882
111578loose thermal19.8310
221568loose thermal8.7510
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 66 -
Rwork0.286 1248 -
obs--98.43 %

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