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- PDB-5smj: Trypanothione reductase -

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Basic information

Entry
Database: PDB / ID: 5smj
TitleTrypanothione reductase
ComponentsN(1),N(8)-bis(glutathionyl)spermidine reductase
KeywordsOXIDOREDUCTASE / Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.65 Å
AuthorsFiorillo, A. / Ilari, A.
Funding supportEuropean Union, Italy, 2items
OrganizationGrant numberCountry
iNEXT-DiscoveryLB25167European Union
CNCCSB56G1500114000 Italy
CitationJournal: Front Mol Biosci / Year: 2022
Title: Innovative Approach for a Classic Target: Fragment Screening on Trypanothione Reductase Reveals New Opportunities for Drug Design.
Authors: Fiorillo, A. / Colotti, G. / Exertier, C. / Liuzzi, A. / Seghetti, F. / Salerno, A. / Caciolla, J. / Ilari, A.
History
DepositionMar 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: N(1),N(8)-bis(glutathionyl)spermidine reductase
B: N(1),N(8)-bis(glutathionyl)spermidine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,55518
Polymers106,9962
Non-polymers2,55916
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-71 kcal/mol
Surface area36170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.560, 108.921, 111.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N(1),N(8)-bis(glutathionyl)spermidine reductase / Trypanothione reductase


Mass: 53497.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3L6KZJ1, trypanothione-disulfide reductase

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Non-polymers , 5 types, 547 molecules

#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD 22%, PEG 3350 14%, imidazole 40 mM pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91264 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91264 Å / Relative weight: 1
ReflectionResolution: 1.65→112.21 Å / Num. obs: 118791 / % possible obs: 98.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allCC1/2Diffraction-IDNet I/σ(I) obs% possible all
1.65-1.681.10956610.2510.996
4.48-112.210.02862951171.2100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6RB5

6rb5


Resolution: 1.65→78.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.799 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5745 4.9 %RANDOM
Rwork0.1928 ---
obs0.194 111135 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.3 Å2 / Biso mean: 25.356 Å2 / Biso min: 10.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0 Å2
2---0.36 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.65→78.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7360 0 153 531 8044
Biso mean--30.89 29.84 -
Num. residues----969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137734
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177398
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.64110516
X-RAY DIFFRACTIONr_angle_other_deg1.4321.57717057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89222.886343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.395151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9451536
X-RAY DIFFRACTIONr_chiral_restr0.080.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021674
X-RAY DIFFRACTIONr_mcbond_it2.142.4353890
X-RAY DIFFRACTIONr_mcbond_other2.1392.4343889
X-RAY DIFFRACTIONr_mcangle_it2.8343.6464863
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 493 -
Rwork0.324 7889 -
all-8382 -
obs--96.36 %

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