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- PDB-2pwp: Crystal structure of spermidine synthase from Plasmodium falcipar... -

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Basic information

Entry
Database: PDB / ID: 2pwp
TitleCrystal structure of spermidine synthase from Plasmodium falciparum in complex with spermidine
ComponentsSpermidine synthase
KeywordsTRANSFERASE / spermidine synthase / spermidine / Structural Genomics Consortium / SGC
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
SPERMIDINE / Spermidine synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsQiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. ...Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Plotnikov, A.N. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermidine.
Authors: Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / ...Authors: Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Zhao, Y. / Schapira, M. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Plotnikov, A.N. / Bochkarev, A. / Hui, R.
History
DepositionMay 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)97,30010
Polymers96,4923
Non-polymers8087
Water5,477304
1
A: Spermidine synthase
hetero molecules

A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8036
Polymers64,3282
Non-polymers4754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8997
Polymers64,3282
Non-polymers5715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-20 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.969, 134.498, 48.711
Angle α, β, γ (deg.)90.00, 95.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

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Components

#1: Protein Spermidine synthase


Mass: 32164.104 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 / Gene: PF11_0301 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-Rosetta Oxford / References: UniProt: Q8II73, spermidine synthase
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% w/v PEG3350, 0.1M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 21, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 74829 / Num. obs: 74737 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.081 / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3746 / Rsym value: 0.65 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.1.19refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HTE

2hte


Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3765 5 %RANDOM
Rwork0.195 ---
all-74737 --
obs-74726 100 %-
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å21.99 Å23.01 Å2
2--0 Å2-0.89 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 53 304 7053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.005
X-RAY DIFFRACTIONr_angle_refined_deg0.692
X-RAY DIFFRACTIONr_chiral_restr0.057
X-RAY DIFFRACTIONr_gen_planes_refined0.003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.318
LS refinement shellResolution: 2.1→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.39 132
Rwork0.346 -
obs-2322

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