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- PDB-6o64: Crystal Structure of Arabidopsis thaliana Spermidine Synthase iso... -

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Basic information

Entry
Database: PDB / ID: 6o64
TitleCrystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 2 (AtSPDS2)
ComponentsSpermidine synthase 2
KeywordsTRANSFERASE / Polyamine metabolism / Putrescine Biosynthesis / dc-SAM / MTA
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Spermidine/spermine synthase, eukaryotes / 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. ...Spermidine/spermine synthase, eukaryotes / 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
ACETATE ION / FORMIC ACID / MALONATE ION / DI(HYDROXYETHYL)ETHER / Spermidine synthase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSekula, B. / Dauter, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)The Intramural Research Program United States
CitationJournal: Front Plant Sci / Year: 2019
Title: Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms FromArabidopsis thaliana.
Authors: Sekula, B. / Dauter, Z.
History
DepositionMar 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spermidine synthase 2
B: Spermidine synthase 2
C: Spermidine synthase 2
D: Spermidine synthase 2
E: Spermidine synthase 2
F: Spermidine synthase 2
G: Spermidine synthase 2
H: Spermidine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,61431
Polymers267,6498
Non-polymers1,96523
Water16,862936
1
A: Spermidine synthase 2
B: Spermidine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2306
Polymers66,9122
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-13 kcal/mol
Surface area21660 Å2
MethodPISA
2
C: Spermidine synthase 2
D: Spermidine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4397
Polymers66,9122
Non-polymers5275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-2 kcal/mol
Surface area20730 Å2
MethodPISA
3
E: Spermidine synthase 2
F: Spermidine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,64811
Polymers66,9122
Non-polymers7369
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-4 kcal/mol
Surface area20660 Å2
MethodPISA
4
G: Spermidine synthase 2
H: Spermidine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2987
Polymers66,9122
Non-polymers3855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-15 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.646, 162.699, 97.494
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Spermidine synthase 2 / SPDSY 2 / Putrescine aminopropyltransferase 2


Mass: 33456.125 Da / Num. of mol.: 8 / Fragment: residues 39-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SPDSYN2, At1g70310, F17O7.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O48661, spermidine synthase

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Non-polymers , 6 types, 959 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen G4 (Carboxylic acids, buffer system 1, precipitant mix 4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 1, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46 Å / Num. obs: 125268 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6263 / CC1/2: 0.844 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSVersion Jan 26, 2018data reduction
STARANISOdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.944 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.193 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23052 1234 1 %RANDOM
Rwork0.17605 ---
obs0.17659 124006 80.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.41 Å2
2---0.36 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→42.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17482 0 131 936 18549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01318043
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716821
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.6324452
X-RAY DIFFRACTIONr_angle_other_deg1.3731.57139196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.39452257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45323.947798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.032152999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.391556
X-RAY DIFFRACTIONr_chiral_restr0.0920.22348
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023523
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_it1.7982.1589054
X-RAY DIFFRACTIONr_mcbond_other1.7982.1589055
X-RAY DIFFRACTIONr_mcangle_it2.953.21311281
X-RAY DIFFRACTIONr_mcangle_other2.953.21411282
X-RAY DIFFRACTIONr_scbond_it1.9952.3958989
X-RAY DIFFRACTIONr_scbond_other1.9962.3948982
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2443.47613166
X-RAY DIFFRACTIONr_long_range_B_refined5.59325.37920066
X-RAY DIFFRACTIONr_long_range_B_other5.55225.23519890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 42 -
Rwork0.25 4786 -
obs--41.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6208-0.0531-0.15510.1269-0.21370.47970.07810.0339-0.0267-0.00630.0610.1011-0.0431-0.0636-0.13910.1048-0.04010.0020.04510.05680.3253.413625.917930.9589
20.2829-0.0530.21860.0572-0.10.3519-0.01750.1055-0.00240.007-0.02920.06170.04150.14310.04670.1476-0.00610.03440.07580.00850.247635.748124.382630.8454
31.1503-0.177-0.08520.0607-0.02190.0494-0.014-0.33840.2031-0.07280.0187-0.02180.09090.0394-0.00470.190.03360.03530.1546-0.11410.160854.195213.163572.1406
41.6905-0.22740.35530.0601-0.12490.29740.032-0.50920.2213-0.07170.0504-0.01110.165-0.0652-0.08240.1573-0.0340.01170.2107-0.17370.235321.494415.547872.7088
50.87650.1479-0.3490.0325-0.01140.5442-0.04580.06820.01550.0040.0089-0.0012-0.0194-0.08090.03690.1710.0265-0.03680.13250.00220.103733.021561.803154.9113
60.68090.2257-0.28640.1641-0.19490.2509-0.0309-0.0726-0.11730.0125-0.0749-0.0627-0.06050.08510.10580.1521-0.0023-0.04540.16640.05950.128165.326663.86155.66
70.346-0.0374-0.36710.0402-0.11391.3333-0.0179-0.1134-0.0674-0.01-0.03680.0322-0.02250.37410.05470.13250.0245-0.02490.30320.02090.059745.89356.216498.4278
80.50060.09880.26180.03660.03110.39120.0248-0.0963-0.13630.0019-0.0093-0.0513-0.1098-0.2773-0.01560.09940.0594-0.02080.3262-0.0090.075713.435856.208197.0063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 501
2X-RAY DIFFRACTION2B31 - 501
3X-RAY DIFFRACTION3C31 - 501
4X-RAY DIFFRACTION4D31 - 501
5X-RAY DIFFRACTION5E31 - 501
6X-RAY DIFFRACTION6F31 - 501
7X-RAY DIFFRACTION7G31 - 501
8X-RAY DIFFRACTION8H31 - 501

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