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- PDB-6bq3: Crystal structure of Medicago truncatula Thermospermine Synthase ... -

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Basic information

Entry
Database: PDB / ID: 6bq3
TitleCrystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with 5'-S-(3-aminopropyl)-5'-thioadenosine
ComponentsThermospermine synthase
KeywordsTRANSFERASE / polyamine biosynthesis / tetraamine / thermospermine / spermidine / aminopropyl transferase
Function / homology
Function and homology information


thermospermine synthase activity / spermidine synthase / spermidine synthase activity / polyamine biosynthetic process
Similarity search - Function
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 ...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'-S-(3-aminopropyl)-5'-thioadenosine / Putative spermidine synthase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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: Biochem. J. / Year: 2018
Title: Crystal structure of thermospermine synthase fromMedicago truncatulaand substrate discriminatory features of plant aminopropyltransferases.
Authors: Sekula, B. / Dauter, Z.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermospermine synthase
B: Thermospermine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2394
Polymers74,5582
Non-polymers6812
Water2,936163
1
A: Thermospermine synthase
B: Thermospermine synthase
hetero molecules

A: Thermospermine synthase
B: Thermospermine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,4788
Polymers149,1164
Non-polymers1,3624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8530 Å2
ΔGint-46 kcal/mol
Surface area43580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.052, 81.052, 163.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thermospermine synthase


Mass: 37279.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7K2D1
#2: Chemical ChemComp-DSH / 5'-S-(3-aminopropyl)-5'-thioadenosine


Mass: 340.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N6O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.8 Å3/Da / Density % sol: 31.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG3350, 0.1 M Magnesium Chloride, 0.1 M MES buffer; cryo 33% PEG400, 10% PEG3350, 0.1 M Magnesium Chloride, Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 18, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→72.59 Å / Num. obs: 43034 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.4
Reflection shellResolution: 1.91→2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5266 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000v716data reduction
HKL-3000v716data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BQ2

6bq2


Resolution: 1.91→72.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.359 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23793 1060 2.5 %RANDOM
Rwork0.18913 ---
obs0.19034 41900 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.91→72.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 46 163 4881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194883
X-RAY DIFFRACTIONr_bond_other_d0.0020.024471
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9186630
X-RAY DIFFRACTIONr_angle_other_deg0.988310416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65624.737228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15615846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1141520
X-RAY DIFFRACTIONr_chiral_restr0.10.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
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_it1.2172.5972360
X-RAY DIFFRACTIONr_mcbond_other1.2172.5962359
X-RAY DIFFRACTIONr_mcangle_it1.8613.8882955
X-RAY DIFFRACTIONr_mcangle_other1.8613.8892956
X-RAY DIFFRACTIONr_scbond_it1.3992.8122523
X-RAY DIFFRACTIONr_scbond_other1.3992.8132524
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2164.1463673
X-RAY DIFFRACTIONr_long_range_B_refined4.19230.7445478
X-RAY DIFFRACTIONr_long_range_B_other4.19230.755479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 71 -
Rwork0.298 3005 -
obs--98.91 %
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)
17.3866-2.9749-0.91612.04470.7591.5139-0.1566-0.1565-0.021-0.04760.05670.23160.0927-0.02420.09990.18150.02010.01660.15460.01040.13923.934616.86926.7101
25.60193.8949-0.30736.7486-1.28171.3901-0.11620.3899-0.3565-0.290.16980.09030.3025-0.0595-0.05360.18730.03710.04620.1470.00860.124826.23016.591111.5342
31.4880.37110.12123.2893-0.91532.2150.06550.0599-0.4018-0.2369-0.0155-0.15360.45820.2293-0.050.12910.0823-0.00560.10360.05290.199326.5750.562728.6986
43.4372-0.14561.34671.9626-0.12673.7966-0.013-0.0238-0.458-0.28270.10810.48540.3215-0.4683-0.09510.1669-0.0051-0.04070.12050.0830.356211.0342-1.67829.3818
51.85880.19790.14183.4423-0.91631.16510.0395-0.2568-0.11020.28830.16730.3928-0.0064-0.1771-0.20680.05380.02760.04960.08470.08150.181313.998312.234433.3197
62.738-1.30043.71536.7355-3.22115.4046-0.1520.18060.07360.5676-0.1693-0.7695-0.35540.32360.32130.2148-0.0016-0.0550.25110.090.226232.308112.344638.245
71.9545-0.7438-0.47372.9699-0.09981.91410.2763-0.1464-0.19280.4368-0.10610.7730.1589-0.3011-0.17030.32350.01380.17140.20850.07740.26299.754418.380632.2241
86.7433-3.2771.76372.9167-2.02384.0062-0.19550.07-0.20780.19640.1053-0.1403-0.04610.1280.09020.2170.034-0.04720.1297-0.06710.136517.519527.77995.0193
93.23983.08320.23358.19530.31522.1816-0.0220.13360.0016-0.247-0.0808-0.0654-0.03310.22980.10270.1180.0367-0.02490.11860.01580.047115.57738.36727.2987
101.53580.20990.07452.08540.0861.6285-0.0921-0.04780.22840.00870.02630.2764-0.1833-0.09270.06580.06410.02730.00120.0157-0.00290.075612.69746.443624.0229
112.05430.43570.29332.89370.26612.8004-0.11980.10790.274-0.10590.0309-0.0652-0.19440.10730.08890.11460.00460.00030.01210.01590.072818.255751.495520.3652
121.90980.2515-0.2233.09610.57041.0787-0.0347-0.24090.07740.15360.0032-0.2519-0.08870.11830.03150.04670.0242-0.02130.07760.00330.036126.003340.745130.2123
131.8062-0.0487-0.93114.54121.18911.06840.0132-0.08210.03160.3582-0.22880.60950.0991-0.2120.21550.17440.04870.11260.1925-0.04520.12769.454435.995134.7912
143.67243.0377-0.10046.7468-0.48991.10340.1547-0.2161-0.02350.2417-0.1237-0.4332-0.0370.264-0.03090.07690.0481-0.01010.16950.00970.109434.678832.556930.0344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 46
2X-RAY DIFFRACTION2A47 - 76
3X-RAY DIFFRACTION3A77 - 167
4X-RAY DIFFRACTION4A168 - 205
5X-RAY DIFFRACTION5A206 - 275
6X-RAY DIFFRACTION6A276 - 287
7X-RAY DIFFRACTION7A288 - 315
8X-RAY DIFFRACTION8B24 - 47
9X-RAY DIFFRACTION9B48 - 76
10X-RAY DIFFRACTION10B77 - 140
11X-RAY DIFFRACTION11B141 - 189
12X-RAY DIFFRACTION12B190 - 274
13X-RAY DIFFRACTION13B275 - 297
14X-RAY DIFFRACTION14B298 - 315

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