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- PDB-5s9v: PanDDA analysis group deposition -- Crystal Structure of Trypanos... -

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Basic information

Entry
Database: PDB / ID: 5s9v
TitlePanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z2856434826
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 / Chem-NUY / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.9 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
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)110,03220
Polymers106,9962
Non-polymers3,03618
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-73 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.030, 108.790, 111.930
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, 545 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-NUY / [4-(propan-2-yl)piperazin-1-yl](thiophen-2-yl)methanone


Mass: 238.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N2OS / 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.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 45.98 % / 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: 1.9→65.1 Å / Num. obs: 77649 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 11.2 / Num. measured all: 518009 / Scaling rejects: 6
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
1.9-1.956.72.2853807456990.330.9492.4770.899.9
8.5-65.16.40.02863789940.9990.0120.0344.699.6

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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: 1.9→65.19 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.579 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 3850 5 %RANDOM
Rwork0.1844 ---
obs0.1866 73722 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.64 Å2 / Biso mean: 41.375 Å2 / Biso min: 19.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å20 Å2
2---0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.9→65.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7360 0 185 527 8072
Biso mean--52.08 45.46 -
Num. residues----969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138861
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178018
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.64511469
X-RAY DIFFRACTIONr_angle_other_deg1.3051.57818510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10551077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07122.487382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.626151379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2261543
X-RAY DIFFRACTIONr_chiral_restr0.0710.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021861
X-RAY DIFFRACTIONr_mcbond_it2.8144.1484402
X-RAY DIFFRACTIONr_mcbond_other2.8154.1394384
X-RAY DIFFRACTIONr_mcangle_it3.8196.1395313
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 312 -
Rwork0.354 5376 -
all-5688 -
obs--99.75 %

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