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- PDB-5s9w: PanDDA analysis group deposition -- Crystal Structure of Trypanos... -

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Basic information

Entry
Database: PDB / ID: 5s9w
TitlePanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z26769872
ComponentsN(1),N(8)-bis(glutathionyl)spermidine reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Diamond I04-1 fragment screening / PanDDA / XChemExplorer / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
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 / ~{N}-[2-(4-fluorophenyl)ethyl]furan-2-carboxamide / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.96 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
DepositionMay 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)110,02120
Polymers106,9962
Non-polymers3,02618
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12060 Å2
ΔGint-68 kcal/mol
Surface area35940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.650, 109.110, 111.970
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 , 6 types, 538 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-N08 / ~{N}-[2-(4-fluorophenyl)ethyl]furan-2-carboxamide


Mass: 233.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12FNO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.9 % / Mosaicity: 0 °
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: 0.9126 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9126 Å / Relative weight: 1
ReflectionResolution: 1.96→78.14 Å / Num. obs: 70595 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.044 / Rrim(I) all: 0.109 / Net I/σ(I): 9.4 / Num. measured all: 406778 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.96-2.014.61.9442351151510.3231.0022.1950.899.8
8.77-78.146.40.04857479030.9980.0210.05331.599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6RB5

6rb5


Resolution: 1.96→78.14 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.554 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3457 4.9 %RANDOM
Rwork0.1963 ---
obs0.1988 67067 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.29 Å2 / Biso mean: 47.175 Å2 / Biso min: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20 Å2
2--2.76 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 1.96→78.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7360 0 187 520 8067
Biso mean--54.6 51.31 -
Num. residues----969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138598
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177829
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.64111223
X-RAY DIFFRACTIONr_angle_other_deg1.2581.57718066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08651044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32922.568370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.079151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1471540
X-RAY DIFFRACTIONr_chiral_restr0.0660.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029391
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021827
X-RAY DIFFRACTIONr_mcbond_it3.2344.7694255
X-RAY DIFFRACTIONr_mcbond_other3.2434.7654232
X-RAY DIFFRACTIONr_mcangle_it4.5387.1235172
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 223 -
Rwork0.384 4907 -
all-5130 -
obs--99.32 %

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