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

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Basic information

Entry
Database: PDB / ID: 4cxm
TitleCrystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with METHYLTHIOADENOSIN AND SPERMIDINE after catalysis in crystal
ComponentsSPERMIDINE SYNTHASE
KeywordsTRANSFERASE / ANINOPROPYL 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
5'-DEOXY-5'-METHYLTHIOADENOSINE / SPERMIDINE / Spermidine synthase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSprenger, J. / 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
DepositionApr 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 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)97,9919
Polymers96,6633
Non-polymers1,3286
Water8,935496
1
B: SPERMIDINE SYNTHASE
C: SPERMIDINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3276
Polymers64,4422
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-6.8 kcal/mol
Surface area21520 Å2
MethodPISA
2
A: SPERMIDINE SYNTHASE
hetero molecules

A: SPERMIDINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3276
Polymers64,4422
Non-polymers8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5080 Å2
ΔGint-6.1 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.900, 134.400, 48.300
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2019-

HOH

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Components

#1: Protein SPERMIDINE SYNTHASE /


Mass: 32221.150 Da / Num. of mol.: 3
Fragment: RESIDUES 41-321 (ACCORDING TO UNIPROT SEQUENCE Q8II73)
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
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT USED FOR CRYSTALLIZATION IS MISSES 40 RESIDUES FROM NATIVE SEQUENCE. RESIDUE LYS 41 ...THE CONSTRUCT USED FOR CRYSTALLIZATION IS MISSES 40 RESIDUES FROM NATIVE SEQUENCE. RESIDUE LYS 41 FROM UNIPROT SEQUENCE IS N-TERMINAL RESIDUE IN THIS STRUCTURE

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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: 3.38 Å3/Da / Density % sol: 63.66 % / Description: NONE
Crystal growDetails: 27 % PEG 3350, 0.1 M MES PH 5.5, 0.1 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04122
DetectorType: MARRESEARCH 65 MM / Detector: CCD / Date: Dec 13, 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: 1.75→50 Å / Num. obs: 124715 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.98
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.29 / % possible all: 98.7

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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→44.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.3 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21554 6255 5 %RANDOM
Rwork0.17902 ---
obs0.18083 118415 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.319 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 90 496 7336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.026993
X-RAY DIFFRACTIONr_bond_other_d0.0010.026722
X-RAY DIFFRACTIONr_angle_refined_deg2.181.989443
X-RAY DIFFRACTIONr_angle_other_deg1.078315585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6225.714294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.258151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.121156
X-RAY DIFFRACTIONr_chiral_restr0.1490.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
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: 1.749→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 441 -
Rwork0.314 8683 -
obs--97.15 %

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