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- PDB-4bp3: Crystal Structure of Plasmodium Falciparum Spermidine Synthase in... -

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Basic information

Entry
Database: PDB / ID: 4bp3
TitleCrystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with DECARBOXYLATED S-ADENOSYLMETHIONINE5' AND 4- METHYLANILINE
ComponentsSPERMIDINE SYNTHASE
KeywordsTRANSFERASE / AMINOPROPYL TRANSFERASE / POLYAMINE PATHWAY / ROSSMANN-LIKE FOLD
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 / 4-METHYLANILINE / Chem-S4M / Spermidine synthase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSprenger, J. / Halander, J.C. / Svensson, B. / Al-Karadaghi, S. / Persson, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Three-Dimensional Structures of Plasmodium Falciparum Spermidine Synthase with Bound Inhibitors Suggest New Strategies for Drug Design
Authors: Sprenger, J. / Svensson, B. / Halander, J. / Carey, J. / Persson, L. / Al-Karadaghi, S.
History
DepositionMay 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)98,65112
Polymers96,6633
Non-polymers1,9879
Water7,044391
1
A: SPERMIDINE SYNTHASE
hetero molecules

A: SPERMIDINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3696
Polymers64,4422
Non-polymers9274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4440 Å2
ΔGint-20 kcal/mol
Surface area21080 Å2
MethodPISA
2
B: SPERMIDINE SYNTHASE
C: SPERMIDINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9669
Polymers64,4422
Non-polymers1,5247
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-9.9 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.460, 132.790, 49.158
Angle α, β, γ (deg.)90.00, 94.86, 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: 32221.150 Da / Num. of mol.: 3 / Fragment: RESIDUES 40-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: P15-TEV-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8II73, spermidine synthase

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Non-polymers , 5 types, 400 molecules

#2: Chemical ChemComp-4MN / 4-METHYLANILINE


Mass: 107.153 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H9N
#3: Chemical ChemComp-S4M / 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE


Mass: 356.444 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H24N6O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.31 Å3/Da / Density % sol: 62.87 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04122
DetectorType: MARRESEARCH 165 MM / Detector: CCD / Date: Jun 27, 2013 / Details: MULTILAYER MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04122 Å / Relative weight: 1
ReflectionResolution: 1.76→28.65 Å / Num. obs: 118398 / % possible obs: 93.7 % / Observed criterion σ(I): 1 / Redundancy: 3.05 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.42
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.39 / % possible all: 78.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I7C

2i7c


Resolution: 1.75→28.66 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.23 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21232 5852 5 %RANDOM
Rwork0.17958 ---
obs0.1812 111410 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.04 Å2
2---0.07 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6739 0 136 391 7266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.027071
X-RAY DIFFRACTIONr_bond_other_d0.0010.026813
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.9879547
X-RAY DIFFRACTIONr_angle_other_deg0.985315797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37725.685292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.239151280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.587156
X-RAY DIFFRACTIONr_chiral_restr0.1480.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021535
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.754→1.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 190 -
Rwork0.332 3845 -
obs--44.15 %

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