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- PDB-5y4q: Crystal structure of Trypanosoma cruzi spermidine synthase in com... -

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Basic information

Entry
Database: PDB / ID: 5y4q
TitleCrystal structure of Trypanosoma cruzi spermidine synthase in complex with N-(4-methoxyphenyl)quinolin-4-amine
ComponentsSpermidine synthase, putative
KeywordsTRANSFERASE / polyamine synthesis
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain ...Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / Spermidine Synthase; Chain: A, domain 2 / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-(4-methoxyphenyl)quinolin-4-amine / Chem-S4M / Spermidine synthase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsAmano, Y. / Tateishi, Y.
CitationJournal: Acs Omega / Year: 2023
Title: Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro , and X-ray Crystallography.
Authors: Yoshino, R. / Yasuo, N. / Hagiwara, Y. / Ishida, T. / Inaoka, D.K. / Amano, Y. / Tateishi, Y. / Ohno, K. / Namatame, I. / Niimi, T. / Orita, M. / Kita, K. / Akiyama, Y. / Sekijima, M.
History
DepositionAug 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 6, 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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spermidine synthase, putative
B: Spermidine synthase, putative
C: Spermidine synthase, putative
D: Spermidine synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,84212
Polymers136,4154
Non-polymers2,4278
Water2,846158
1
A: Spermidine synthase, putative
B: Spermidine synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4216
Polymers68,2072
Non-polymers1,2134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-24 kcal/mol
Surface area21000 Å2
MethodPISA
2
C: Spermidine synthase, putative
D: Spermidine synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4216
Polymers68,2072
Non-polymers1,2134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-23 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.977, 99.665, 134.503
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Spermidine synthase, putative


Mass: 34103.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053510339.50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DA73, spermidine synthase
#2: Chemical
ChemComp-S4M / 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE


Mass: 356.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H24N6O3S
#3: Chemical
ChemComp-8OF / N-(4-methoxyphenyl)quinolin-4-amine


Mass: 250.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris, Ammonium sulfate, PEG 4000 / PH range: 5.5 - 6.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 70814 / % possible obs: 98.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.2
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1S

5b1s


Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.358 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.26927 3524 5 %RANDOM
Rwork0.2413 ---
obs0.24277 66426 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.25 Å2
2--0.15 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8661 0 172 158 8991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9812261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74851081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38923.783415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.737151501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5061560
X-RAY DIFFRACTIONr_chiral_restr0.1160.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217116
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9223.4354367
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9525.1285431
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5433.8164683
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.36447.8813565
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 277 -
Rwork0.305 4959 -
obs--99.9 %

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