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- PDB-3b7p: Crystal structure of spermidine synthase from Plasmodium falcipar... -

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Basic information

Entry
Database: PDB / ID: 3b7p
TitleCrystal structure of spermidine synthase from Plasmodium falciparum in complex with spermine
ComponentsSpermidine synthase
KeywordsTRANSFERASE / spermidine synthase / spermine / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Metabolism of polyamines / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / 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 / SPERMINE / 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. / 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 spermine.
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
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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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)98,1629
Polymers96,6633
Non-polymers1,4996
Water10,341574
1
A: Spermidine synthase
hetero molecules

A: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4426
Polymers64,4422
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2900 Å2
MethodPISA
2
B: Spermidine synthase
C: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4426
Polymers64,4422
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.483, 134.584, 48.370
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

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Components

#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 / 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-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% w/v PEG 3350, 0.1M Ammonium sulfate, 0.1M Bis-tris, pH 5.5, VAPOR DIFFUSION, 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: May 27, 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→30 Å / Num. all: 84798 / Num. obs: 84798 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 16.67
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.21 / Num. unique all: 7768 / Rsym value: 0.472 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PWP
Resolution: 2→29.44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.724 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24978 4239 5 %RANDOM
Rwork0.21458 ---
obs0.21634 80454 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.564 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.06 Å2
2---0.05 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6753 0 102 574 7429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227080
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.989578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08125.814301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.082151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.62156
X-RAY DIFFRACTIONr_chiral_restr0.0950.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025191
X-RAY DIFFRACTIONr_nbd_refined0.1960.23412
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2476
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.223
X-RAY DIFFRACTIONr_mcbond_it0.6621.54372
X-RAY DIFFRACTIONr_mcangle_it1.12426910
X-RAY DIFFRACTIONr_scbond_it1.65733146
X-RAY DIFFRACTIONr_scangle_it2.5114.52656
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 303 -
Rwork0.349 5580 -
obs--93.95 %

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