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- PDB-4yv0: Crystal structure of Trypanosoma cruzi spermidine synthase in com... -

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Basic information

Entry
Database: PDB / ID: 4yv0
TitleCrystal structure of Trypanosoma cruzi spermidine synthase in complex with (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine- 2-carboxamid
ComponentsSpermidine synthase, putative
KeywordsTRANSFERASE / methyltransferase / 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
Chem-4JW / Chem-S4M / Spermidine synthase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAmano, Y. / Tateishi, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase
Authors: Amano, Y. / Namatame, I. / Tateishi, Y. / Honboh, K. / Tanabe, E. / Niimi, T. / Sakashita, H.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Structure summary
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)138,37910
Polymers136,4154
Non-polymers1,9646
Water4,972276
1
A: Spermidine synthase, putative
B: Spermidine synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1905
Polymers68,2072
Non-polymers9823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-23 kcal/mol
Surface area20690 Å2
MethodPISA
2
C: Spermidine synthase, putative
D: Spermidine synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1905
Polymers68,2072
Non-polymers9823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-23 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.560, 99.783, 135.005
Angle α, β, γ (deg.)90.00, 90.64, 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-4JW / (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine-2-carboxamide


Mass: 269.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG4000, ammonium sulfate, bis-Tris / PH range: 5.5 - 6.5

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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: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→29.61 Å / Num. obs: 76898 / % possible obs: 96.26 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4.3 / % possible all: 94.87

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BWB

3bwb


Resolution: 1.95→29.41 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.499 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25251 4047 5 %RANDOM
Rwork0.20791 ---
obs0.21023 76897 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.191 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8837 0 136 276 9249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199199
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.97812476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89151114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44523.765417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.457151519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4511560
X-RAY DIFFRACTIONr_chiral_restr0.1480.21364
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217118
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_it2.6792.6824484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5943.9985586
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8463.074715
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.01423.2814077
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 284 -
Rwork0.26 5559 -
obs--94.87 %

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