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- PDB-2hte: The crystal structure of spermidine synthase from p. falciparum i... -

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Basic information

Entry
Database: PDB / ID: 2hte
TitleThe crystal structure of spermidine synthase from p. falciparum in complex with 5'-methylthioadenosine
ComponentsSpermidine synthase
KeywordsTRANSFERASE / spermidine synthase / 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
Chem-1PG / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Spermidine synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsQiu, W. / Dong, A. / Ren, H. / Wu, H. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. ...Qiu, W. / Dong, A. / Ren, H. / Wu, H. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Plotnikov, A.N. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: 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)98,15622
Polymers96,6633
Non-polymers1,49319
Water10,287571
1
A: Spermidine synthase
hetero molecules

A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,54216
Polymers64,4422
Non-polymers1,09914
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)65,38514
Polymers64,4422
Non-polymers94312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-22 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.061, 134.600, 48.336
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe biological assembly is a dimer.

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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
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

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Non-polymers , 5 types, 590 molecules

#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 571 / 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: 62.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% w/v PEG3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, 4 mM 5'-methylthioadenosine, pH 5.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 84688 / Num. obs: 82781 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 28.99 Å2 / Rsym value: 0.108 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.48 / Num. unique all: 3421 / Rsym value: 0.877 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZDZ

1zdz
PDB Unreleased entry


Resolution: 2→33.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.769 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23122 4135 5 %RANDOM
Rwork0.1855 ---
all0.192 79849 --
obs0.18782 78619 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.989 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6616 0 106 571 7293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226991
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9849463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52625.791297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.498151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.514156
X-RAY DIFFRACTIONr_chiral_restr0.1210.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025108
X-RAY DIFFRACTIONr_nbd_refined0.2060.23148
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2519
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.226
X-RAY DIFFRACTIONr_mcbond_it1.0581.54324
X-RAY DIFFRACTIONr_mcangle_it1.69526800
X-RAY DIFFRACTIONr_scbond_it2.55833136
X-RAY DIFFRACTIONr_scangle_it3.8424.52640
LS refinement shellResolution: 2→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 267 -
Rwork0.278 5636 -
obs--95.47 %

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