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- PDB-6qmm: Crystal structure of Synecochoccus Spermidine Synthase in complex... -

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Basic information

Entry
Database: PDB / ID: 6qmm
TitleCrystal structure of Synecochoccus Spermidine Synthase in complex with putrescine, spermidine and MTA
Components(Polyamine aminopropyltransferase) x 2
KeywordsTRANSFERASE / Synthase / Homodimer
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytoplasm
Similarity search - Function
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 / Vaccinia Virus protein VP39 ...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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / 1,4-DIAMINOBUTANE / Chem-PXN / SPERMIDINE / Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGuedez, G. / Pothipongsa, A. / Incharoensakdi, A. / Salminen, T.A.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: Biochem.J. / Year: 2019
Title: Crystal structure of dimericSynechococcusspermidine synthase with bound polyamine substrate and product.
Authors: Guedez, G. / Pothipongsa, A. / Siren, S. / Liljeblad, A. / Jantaro, S. / Incharoensakdi, A. / Salminen, T.A.
History
DepositionFeb 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyamine aminopropyltransferase
B: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6976
Polymers62,7972
Non-polymers8994
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint1 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.640, 63.820, 73.500
Angle α, β, γ (deg.)90.000, 92.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Polyamine aminopropyltransferase / Putrescine aminopropyltransferase / PAPT / Spermidine synthase / SPDSY


Mass: 31451.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: speE, Synpcc7942_0628 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q31QK9, spermidine synthase
#2: Protein Polyamine aminopropyltransferase / Putrescine aminopropyltransferase / PAPT / Spermidine synthase / SPDSY


Mass: 31346.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Strain: PCC 7942 / Gene: speE, Synpcc7942_0628 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q31QK9, spermidine synthase

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Non-polymers , 5 types, 260 molecules

#3: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O8
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 45 % v/v Pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.18→48.17 Å / Num. obs: 27391 / % possible obs: 99 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.0721 / Rrim(I) all: 0.083 / Net I/σ(I): 16.18
Reflection shellResolution: 2.18→2.27 Å / Rmerge(I) obs: 0.226 / CC1/2: 0.956 / Rrim(I) all: 0.261

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YUV

4yuv


Resolution: 2.18→48.17 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1375 5 %RANDOM
Rwork0.1416 ---
obs0.1441 26118 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.54 Å2 / Biso mean: 17.36 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20.43 Å2
2---0.07 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 2.18→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4411 0 61 256 4728
Biso mean--38.54 24.34 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0134590
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174154
X-RAY DIFFRACTIONr_angle_refined_deg2.4891.6536252
X-RAY DIFFRACTIONr_angle_other_deg2.6181.5879588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4235554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97121.679262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8815685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3291536
X-RAY DIFFRACTIONr_chiral_restr0.1270.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.025184
X-RAY DIFFRACTIONr_gen_planes_other0.0320.021040
X-RAY DIFFRACTIONr_mcbond_it1.2621.6992225
X-RAY DIFFRACTIONr_mcbond_other1.2631.6992224
X-RAY DIFFRACTIONr_mcangle_it2.0932.542776
LS refinement shellResolution: 2.181→2.238 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 91 -
Rwork0.178 1724 -
all-1815 -
obs--88.02 %

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