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- PDB-6o65: Crystal Structure of Arabidopsis thaliana Spermidine Synthase iso... -

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Basic information

Entry
Database: PDB / ID: 6o65
TitleCrystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1) in complex with decarboxylated S-adenosylmethionine and cyclohexylamine
ComponentsSpermidine synthase 1
KeywordsTRANSFERASE / Polyamine metabolism / Putrescine Biosynthesis / dc-SAM / MTA
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / spermidine biosynthetic process
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
CYCLOHEXYLAMMONIUM ION / DI(HYDROXYETHYL)ETHER / Chem-S4M / Spermidine synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1
B: Spermidine synthase 1
C: Spermidine synthase 1
D: Spermidine synthase 1
E: Spermidine synthase 1
F: Spermidine synthase 1
G: Spermidine synthase 1
H: Spermidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,71732
Polymers266,3448
Non-polymers4,37424
Water37,8862103
1
A: Spermidine synthase 1
B: Spermidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5957
Polymers66,5862
Non-polymers1,0095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-23 kcal/mol
Surface area21270 Å2
MethodPISA
2
C: Spermidine synthase 1
D: Spermidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5957
Polymers66,5862
Non-polymers1,0095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-23 kcal/mol
Surface area21490 Å2
MethodPISA
3
E: Spermidine synthase 1
F: Spermidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7639
Polymers66,5862
Non-polymers1,1787
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-17 kcal/mol
Surface area21200 Å2
MethodPISA
4
G: Spermidine synthase 1
H: Spermidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7639
Polymers66,5862
Non-polymers1,1787
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-18 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.201, 107.558, 142.424
Angle α, β, γ (deg.)90.00, 95.30, 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 1 / SPDSY 1 / Putrescine aminopropyltransferase 1


Mass: 33292.957 Da / Num. of mol.: 8 / Fragment: residues 34-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SPDSYN1, At1g23820, F5O8.38 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZUB3, spermidine synthase

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Non-polymers , 6 types, 2127 molecules

#2: Chemical
ChemComp-S4M / 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE


Mass: 356.444 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H24N6O3S
#3: Chemical
ChemComp-HAI / CYCLOHEXYLAMMONIUM ION


Mass: 100.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14N
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2103 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.18 M ammonium sulfate, 0.09 M BIS-TRIS, 22% PEG 3350, cryoprotection 25% MPD

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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: Feb 15, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.6 Å / Num. obs: 200872 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 10041 / CC1/2: 0.833 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHASER2.8.2phasing
STARANISOdata scaling
XDSVersion Jan 26, 2018data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.6 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.636 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26095 1621 0.8 %RANDOM
Rwork0.21871 ---
obs0.21905 201969 81.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å20.19 Å2
2---0.2 Å2-0 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17981 0 290 2103 20374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01318838
X-RAY DIFFRACTIONr_bond_other_d0.0090.01717517
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.63525605
X-RAY DIFFRACTIONr_angle_other_deg1.5481.57440888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98252351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70224.053834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.999153064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0471556
X-RAY DIFFRACTIONr_chiral_restr0.1070.22448
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0220786
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023654
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_it1.1351.0339358
X-RAY DIFFRACTIONr_mcbond_other1.1351.0339356
X-RAY DIFFRACTIONr_mcangle_it1.7361.53811668
X-RAY DIFFRACTIONr_mcangle_other1.7361.53911669
X-RAY DIFFRACTIONr_scbond_it1.3641.1359480
X-RAY DIFFRACTIONr_scbond_other1.351.1319465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0571.6513897
X-RAY DIFFRACTIONr_long_range_B_refined5.32113.64621951
X-RAY DIFFRACTIONr_long_range_B_other5.22912.96421434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 72 -
Rwork0.264 8190 -
obs--44.96 %
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)
10.06950.10810.10670.17370.16390.3795-0.00610.0009-0.0251-0.02270.0214-0.0305-0.0465-0.04-0.01540.0588-0.004-0.030.1303-0.00510.10441.8574-7.2225-14.1281
20.03460.01860.11350.13150.03810.3971-0.0018-0.0272-0.00230.00460.0246-0.03130.0142-0.0586-0.02290.0680.022-0.04660.14480.00060.08624.0498-2.041117.6721
30.08260.0945-0.10330.1129-0.11970.3926-0.00570.00940.0179-0.0062-0.01090.01250.04430.00610.01660.0726-0.0038-0.02530.1358-0.0040.0872-6.0824-3.935956.7177
40.03940.0512-0.11310.1687-0.07890.37670.0093-0.00270.00030.01070.0140.0024-0.01960.0128-0.02330.0661-0.0022-0.02350.1293-0.00650.1023-14.1922-9.539387.5319
50.13670.27490.21670.57770.31930.9419-0.02720.038-0.0069-0.04810.0617-0.0083-0.08030.0876-0.03450.1088-0.00820.00110.0532-0.00740.001846.7996-2.4816-14.109
60.06860.11150.19550.62370.12840.7767-0.0003-0.0131-0.00280.04880.03670.01290.04880.009-0.03630.12770.0171-0.0110.0545-0.0070.003948.78992.894717.6708
70.20340.2948-0.30830.5794-0.21460.8279-0.04570.03220.0021-0.06390.03940.00660.0845-0.04630.00620.1147-0.00930.01110.04540.00710.002738.64960.483656.5717
80.1130.1052-0.25950.5913-0.07870.7006-0.0088-0.01750.00320.03960.02340.0133-0.00040.0053-0.01460.11470.01090.020.05990.00620.004130.7171-4.796987.528
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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