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- PDB-6i1n: Plasmodium falciparum spermidine synthase in complex with N-(3-am... -

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Basic information

Entry
Database: PDB / ID: 6i1n
TitlePlasmodium falciparum spermidine synthase in complex with N-(3-aminopropyl)-trans-cyclohexane-1,4-diamine
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 / trans-N-(3-aminopropyl)cyclohexane-1,4-diamine / Spermidine synthase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85000131459 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 N-(3-aminopropyl)-trans-cyclohexane-1,4-diamine
Authors: Sprenger, J. / Coertzen, D. / Persson, L. / Carey, J. / Birkholtz, L.M. / Louw, B.I.
History
DepositionOct 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release

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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)111,46712
Polymers109,9213
Non-polymers1,5459
Water8,881493
1
A: Spermidine synthase
hetero molecules

A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1286
Polymers73,2812
Non-polymers8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4060 Å2
ΔGint-4 kcal/mol
Surface area22350 Å2
MethodPISA
2
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4039
Polymers73,2812
Non-polymers1,1227
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-16 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.752, 134.877, 48.647
Angle α, β, γ (deg.)90.000, 95.009, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21A-626-

HOH

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Components

#1: Protein Spermidine synthase /


Mass: 36640.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1129000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8II73, spermidine synthase
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#3: Chemical
ChemComp-JFQ / trans-N-(3-aminopropyl)cyclohexane-1,4-diamine


Mass: 171.283 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H21N3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: 1.8→48.461 Å / Num. obs: 116743 / % possible obs: 99.5 % / Redundancy: 3.807 % / Biso Wilson estimate: 34.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.069 / Χ2: 1.057 / Net I/σ(I): 12.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.853.7381.5150.7783880.4431.76697.5
1.85-1.93.621.0891.0984210.5761.2899.8
1.9-1.953.720.831.582280.7140.97199.5
1.95-2.013.9540.6541.9879130.8170.75699.8
2.01-2.083.9310.4832.6877090.880.5699.7
2.08-2.153.8730.3433.6274340.9330.39999.8
2.15-2.233.8040.2914.2872060.9430.3499.8
2.23-2.323.5380.2235.3269690.9610.26399.2
2.32-2.433.9150.1697.1866450.9810.19699.9
2.43-2.543.9330.1458.5763360.9840.16799.7
2.54-2.683.9350.1110.8260630.9910.12799.8
2.68-2.843.8540.08713.4157230.9940.10299.8
2.84-3.043.5810.06217.553880.9960.07399.7
3.04-3.283.9680.04923.6849690.9980.05799.7
3.28-3.63.9650.03631.5846270.9990.04199.6
3.6-4.023.7990.02938.8241810.9990.03399.4
4.02-4.643.5230.02343.6236650.9990.02799
4.64-5.693.9880.02148.731240.9990.02599.7
5.69-8.043.7580.02246.6524250.9990.02599.3
8.04-48.4613.7280.01457.7132910.01798.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85000131459→48.46 Å / SU ML: 0.265402646339 / Cross valid method: THROUGHOUT / σ(F): 1.34020245478 / Phase error: 30.011165809
RfactorNum. reflection% reflection
Rfree0.225897104255 5478 5.09652509653 %
Rwork0.190698581944 --
obs0.192435484172 107485 99.4936685427 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.2023471039 Å2
Refinement stepCycle: LAST / Resolution: 1.85000131459→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 106 493 7137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01188429928326788
X-RAY DIFFRACTIONf_angle_d1.034043605969131
X-RAY DIFFRACTIONf_chiral_restr0.06544007157431015
X-RAY DIFFRACTIONf_plane_restr0.006746392462971122
X-RAY DIFFRACTIONf_dihedral_angle_d3.925843019614604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.4735603271871940.4441892485663442X-RAY DIFFRACTION99.2087312415
1.871-1.8930.4015362602311620.406165726513339X-RAY DIFFRACTION99.2346938776
1.893-1.91610.4659013238611700.3886382778183365X-RAY DIFFRACTION99.3815012651
1.9161-1.94040.4244561162571900.3645322981963407X-RAY DIFFRACTION98.9273927393
1.9404-1.96590.3638759814931830.3373912722713397X-RAY DIFFRACTION99.6104618809
1.9659-1.99280.3535377459411890.3297233093993365X-RAY DIFFRACTION99.4125874126
1.9928-2.02130.3844510914381770.3156504544593417X-RAY DIFFRACTION99.4465965689
2.0213-2.05150.359736183431860.2900566981633356X-RAY DIFFRACTION99.6062992126
2.0515-2.08350.3097924316821890.2795947441733361X-RAY DIFFRACTION99.3562832354
2.0835-2.11770.3040589510271890.2515059812883425X-RAY DIFFRACTION99.6415770609
2.1177-2.15420.2669610194971900.2383200306933347X-RAY DIFFRACTION99.7743300423
2.1542-2.19340.3019267162452000.2365664468763439X-RAY DIFFRACTION99.8080087767
2.1934-2.23560.2948292284521570.2318235196733388X-RAY DIFFRACTION99.7748381649
2.2356-2.28120.2497111089022060.2229976903053389X-RAY DIFFRACTION99.1997792494
2.2812-2.33080.2630694352591600.2242910656243411X-RAY DIFFRACTION99.0019406709
2.3308-2.3850.2868082793232020.2063729586883331X-RAY DIFFRACTION99.7459062676
2.385-2.44470.2482365370981970.1989706703353446X-RAY DIFFRACTION99.8082191781
2.4447-2.51080.2595941501321930.2049453018383367X-RAY DIFFRACTION99.7198879552
2.5108-2.58460.2351270300681990.1976358457733378X-RAY DIFFRACTION99.6378830084
2.5846-2.66810.2542764589181750.187959427173415X-RAY DIFFRACTION99.9443207127
2.6681-2.76340.2276194190451930.1872705519783403X-RAY DIFFRACTION99.8057174577
2.7634-2.8740.2001309450251730.1781514927773446X-RAY DIFFRACTION99.696969697
2.874-3.00480.2241827218421760.1783826977033410X-RAY DIFFRACTION99.6111111111
3.0048-3.16320.1941552910811780.1845749526163391X-RAY DIFFRACTION99.7484628284
3.1632-3.36140.2434244179851650.1793521403583422X-RAY DIFFRACTION99.6388888889
3.3614-3.62080.1850376048331850.1683881477123435X-RAY DIFFRACTION99.6970531534
3.6208-3.9850.1984763703221770.1554311730743411X-RAY DIFFRACTION99.3630573248
3.985-4.56130.1869651244281660.1474499421613414X-RAY DIFFRACTION99.0592141671
4.5613-5.74530.1435291437751810.1461454906663440X-RAY DIFFRACTION99.5600769865
5.7453-48.47780.1958567200841760.1711259561353450X-RAY DIFFRACTION98.5326086957

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