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- PDB-6bq7: Crystal structure of Medicago truncatula Thermospermine Synthase ... -

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Basic information

Entry
Database: PDB / ID: 6bq7
TitleCrystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with spermidine
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
SPERMIDINE / Putative spermidine synthase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,8494
Polymers74,5582
Non-polymers2902
Water2,036113
1
A: Thermospermine synthase
B: Thermospermine synthase
hetero molecules

A: Thermospermine synthase
B: Thermospermine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6978
Polymers149,1164
Non-polymers5814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10610 Å2
ΔGint-19 kcal/mol
Surface area44240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.962, 79.962, 163.532
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) / Tissue: Leaves / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7K2D1
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1.75 Å3/Da / Density % sol: 29.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG3350, 0.1 M Magnesium Chloride, 0.1 M Bis-Tris propane buffer cryo 33% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→39.24 Å / Num. obs: 39529 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 207
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 6238 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSMay 1, 2016data reduction
XDSNov 1, 2016data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BQ2

6bq2


Resolution: 1.95→39.24 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.86
RfactorNum. reflection% reflection
Rfree0.2437 1026 2.6 %
Rwork0.1876 --
obs0.1891 39438 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 20 113 4796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074813
X-RAY DIFFRACTIONf_angle_d0.9156517
X-RAY DIFFRACTIONf_dihedral_angle_d7.873998
X-RAY DIFFRACTIONf_chiral_restr0.056720
X-RAY DIFFRACTIONf_plane_restr0.006832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9488-2.05150.3241420.30625354X-RAY DIFFRACTION99
2.0515-2.180.33121450.27125399X-RAY DIFFRACTION100
2.18-2.34830.29211440.24945390X-RAY DIFFRACTION100
2.3483-2.58460.29341460.23495449X-RAY DIFFRACTION100
2.5846-2.95850.28371460.22335469X-RAY DIFFRACTION100
2.9585-3.7270.24531480.18935546X-RAY DIFFRACTION100
3.727-39.25120.20681550.14885805X-RAY DIFFRACTION100
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)
11.49351.3113-0.32726.4926-0.21573.2150.07260.34770.1936-0.7042-0.0920.17090.0286-0.36250.00530.40940.06450.01740.44990.03590.364823.69857.77885.5859
21.85550.53450.19063.75950.17885.19670.0401-0.0143-0.34270.17910.0598-0.16440.684-0.1665-0.10490.335-0.0112-0.04090.32890.00770.364925.9395-8.092222.2027
37.10251.8248-1.82717.35810.20493.714-0.12430.5212-0.1844-0.6916-0.0111.31240.3672-1.6999-0.08410.5523-0.1106-0.14880.93020.02060.56447.5969-6.612921.2527
41.3375-0.13780.26314.5685-0.43713.8705-0.0208-0.2299-0.08240.49790.07610.28230.0991-0.7405-0.05970.33470.01040.02610.54970.01390.306116.66332.984931.4912
51.7731-0.42940.81073.0333-0.30973.3056-0.4201-0.23910.13110.58040.43230.0514-0.7702-0.4607-0.00690.64980.307-0.03020.5582-0.06750.417914.830132.902620.8529
62.04490.16511.4213.3883-0.10782.7453-0.2980.01920.48550.45810.1737-0.4415-1.1343-0.37850.00381.0910.3638-0.10770.577-0.09470.619720.496643.126626.3676
71.1319-0.160.6774.69820.24521.9248-0.3825-0.46640.08541.00840.3334-0.6736-0.8243-0.6817-0.07210.80040.3288-0.18640.5321-0.12950.417324.795428.827734.7055
80.6069-0.38660.23354.57390.58744.2338-0.2632-0.10550.62510.82680.3908-0.5416-0.5973-0.7042-0.14110.60270.2224-0.10940.4701-0.00890.518624.015122.765533.3877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 315 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 131 )
6X-RAY DIFFRACTION6chain 'B' and (resid 132 through 199 )
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 279 )
8X-RAY DIFFRACTION8chain 'B' and (resid 280 through 314 )

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