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- PDB-6hy1: Plasmodium falciparum spermidine synthase in complex with 5'-meth... -

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Basic information

Entry
Database: PDB / ID: 6hy1
TitlePlasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal
ComponentsSpermidine synthase
KeywordsTRANSFERASE / Inhibitor complex / catalysis / kinetics
Function / homology
Function and homology information


Metabolism of polyamines / 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-1PG / N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine / trans-N-(3-aminopropyl)cyclohexane-1,4-diamine / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Spermidine synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSprenger, J. / Coertzen, D. / Persson, L. / Carey, J. / Birkholtz, L.M. / Louw, B.I.
CitationJournal: To Be Published
Title: Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal
Authors: Sprenger, J. / Coertzen, D. / Persson, L. / Carey, J. / Birkholtz, L.M. / Louw, B.I.
History
DepositionOct 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,90018
Polymers96,2313
Non-polymers2,66915
Water14,124784
1
A: Spermidine synthase
hetero molecules

A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,89410
Polymers64,1542
Non-polymers1,7408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6270 Å2
ΔGint-3 kcal/mol
Surface area20990 Å2
MethodPISA
2
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,95313
Polymers64,1542
Non-polymers1,79911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-19 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.870, 135.000, 48.570
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Spermidine synthase


Mass: 32077.021 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1129000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8II73, spermidine synthase

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Non-polymers , 6 types, 799 molecules

#2: Chemical ChemComp-GXQ / N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine


Mass: 228.378 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H28N4
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-JFQ / trans-N-(3-aminopropyl)cyclohexane-1,4-diamine


Mass: 171.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H21N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 3350, 0.1M ammonium sulfate, 0.1M 2-(N-morpholino) ethanesulfonic acid, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9299 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9299 Å / Relative weight: 1
ReflectionResolution: 1.55→111.68 Å / Num. obs: 175421 / % possible obs: 94.3 % / Redundancy: 6.833 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 1.075 / Net I/σ(I): 16.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.594.9551.6370.8771880.431.82852.4
1.59-1.636.7281.2371.47123170.6871.3491.5
1.63-1.687.211.031.88125940.8141.10996.8
1.68-1.737.1530.7852.47122810.8830.84697.3
1.73-1.797.0480.5743.28119120.9250.61997.5
1.79-1.856.6460.4284.18115840.9480.46597.8
1.85-1.927.0870.3095.89111620.9770.33497.8
1.92-27.2250.2347.99108030.9860.25298
2-2.097.1070.17110.46103720.9920.18498.1
2.09-2.196.8830.12413.6699370.9950.13498.5
2.19-2.316.5520.10515.7694780.9960.11598.4
2.31-2.457.2350.08320.5389660.9980.08998.7
2.45-2.616.9870.07223.5684110.9980.07898.7
2.61-2.826.7810.05728.8978930.9980.06298.8
2.82-3.096.6750.04435.9772750.9990.04899.2
3.09-3.466.8640.03644.9766020.9990.03999.3
3.46-3.996.5220.0352.6957910.9990.03299.1
3.99-4.896.2860.02556.949310.9990.02799.2
4.89-6.926.7420.02457.9838210.9990.02699.2
6.92-111.686.4820.01962.08210310.02198.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→32.167 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 8308 5.05 %RANDOM
Rwork0.1757 ---
obs0.177 164672 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→32.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 180 784 7713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147075
X-RAY DIFFRACTIONf_angle_d1.2329532
X-RAY DIFFRACTIONf_dihedral_angle_d14.8864203
X-RAY DIFFRACTIONf_chiral_restr0.0861057
X-RAY DIFFRACTIONf_plane_restr0.0091168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.43922630.39064949X-RAY DIFFRACTION93
1.6182-1.63720.39822690.34935084X-RAY DIFFRACTION96
1.6372-1.65720.32142770.33125124X-RAY DIFFRACTION97
1.6572-1.67820.33062790.30275221X-RAY DIFFRACTION97
1.6782-1.70020.2793050.28625090X-RAY DIFFRACTION97
1.7002-1.72350.30462810.26825157X-RAY DIFFRACTION97
1.7235-1.74820.2682740.25485161X-RAY DIFFRACTION97
1.7482-1.77420.28322810.24365158X-RAY DIFFRACTION97
1.7742-1.8020.25032520.23825241X-RAY DIFFRACTION97
1.802-1.83150.26522810.23815138X-RAY DIFFRACTION98
1.8315-1.86310.26052400.22955222X-RAY DIFFRACTION97
1.8631-1.8970.24122690.21235161X-RAY DIFFRACTION98
1.897-1.93340.22492630.20095235X-RAY DIFFRACTION98
1.9334-1.97290.22492650.19965201X-RAY DIFFRACTION98
1.9729-2.01580.25342860.19555237X-RAY DIFFRACTION98
2.0158-2.06270.20052880.18515182X-RAY DIFFRACTION98
2.0627-2.11430.22082690.17955302X-RAY DIFFRACTION98
2.1143-2.17140.21162740.18355159X-RAY DIFFRACTION98
2.1714-2.23530.22172850.19125247X-RAY DIFFRACTION98
2.2353-2.30740.22532640.18875278X-RAY DIFFRACTION98
2.3074-2.38990.19542850.17575205X-RAY DIFFRACTION99
2.3899-2.48550.20112890.17945226X-RAY DIFFRACTION99
2.4855-2.59860.21312780.17445292X-RAY DIFFRACTION99
2.5986-2.73550.19492740.1755262X-RAY DIFFRACTION99
2.7355-2.90680.20322780.16755259X-RAY DIFFRACTION99
2.9068-3.13110.18332890.17065294X-RAY DIFFRACTION99
3.1311-3.44580.20012800.1715314X-RAY DIFFRACTION99
3.4458-3.94370.16813040.14915271X-RAY DIFFRACTION99
3.9437-4.96570.1462480.12965355X-RAY DIFFRACTION99
4.9657-32.1730.17263180.15065339X-RAY DIFFRACTION99

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