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- PDB-6bq2: Crystal structure of Medicago truncatula Thermospermine Synthase ... -

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Basic information

Entry
Database: PDB / ID: 6bq2
TitleCrystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS)
ComponentsThermospermine synthase ACAULIS protein
KeywordsTRANSFERASE / polyamine biosynthesis / tetraamine / thermospermine / spermidine / aminopropyl transferase
Function / homology
Function and homology information


thermospermine synthase / thermospermine synthase activity / polyamine biosynthetic process / spermidine synthase activity
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
thermospermine synthase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 ACAULIS protein
B: Thermospermine synthase ACAULIS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6695
Polymers74,5582
Non-polymers1113
Water5,441302
1
A: Thermospermine synthase ACAULIS protein
B: Thermospermine synthase ACAULIS protein
hetero molecules

A: Thermospermine synthase ACAULIS protein
B: Thermospermine synthase ACAULIS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,33810
Polymers149,1164
Non-polymers2216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9580 Å2
ΔGint-70 kcal/mol
Surface area44310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.530, 80.530, 164.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-668-

HOH

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Components

#1: Protein Thermospermine synthase ACAULIS protein


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 / Gene: 11439099, MTR_5g006140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7K2D1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.79 Å3/Da / Density % sol: 31.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG3350, 0.1 M Magnesium Chloride and 0.1 M MES buffer; cryo 33% PEG400

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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: Mar 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: 1.68→46.81 Å / Num. obs: 62270 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.9
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.058 / Mean I/σ(I) obs: 2 / Num. unique obs: 9765 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSMay 1, 2016data reduction
XSCALENov 1, 2016data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1INL

1inl


Resolution: 1.68→46.81 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.253 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21671 1059 1.7 %RANDOM
Rwork0.17557 ---
obs0.17626 61210 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.349 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.68→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 6 302 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194798
X-RAY DIFFRACTIONr_bond_other_d0.0020.024507
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9526492
X-RAY DIFFRACTIONr_angle_other_deg1.284310426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85924.714227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58815839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2691520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025371
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021069
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_it1.2932.1852333
X-RAY DIFFRACTIONr_mcbond_other1.2922.1842332
X-RAY DIFFRACTIONr_mcangle_it2.1343.2672915
X-RAY DIFFRACTIONr_mcangle_other2.1343.2682916
X-RAY DIFFRACTIONr_scbond_it1.7782.472465
X-RAY DIFFRACTIONr_scbond_other1.7772.472465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9453.5883577
X-RAY DIFFRACTIONr_long_range_B_refined5.37818.2465530
X-RAY DIFFRACTIONr_long_range_B_other5.37818.2535531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.679→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 74 -
Rwork0.284 4287 -
obs--96.57 %
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)
14.0834-1.4580.32291.5517-0.21830.1329-0.1969-0.17970.1543-0.1330.12680.08540.05770.05730.07010.08070.03350.00420.09660.04890.076523.411816.18456.8019
22.03941.5692-0.46093.5953-1.5450.6989-0.11090.2201-0.0618-0.16760.13940.02590.077-0.0395-0.02850.1008-0.01950.01770.08670.01440.025725.92235.476811.297
30.0172-0.0716-0.00431.0447-0.46370.82930.0135-0.0068-0.0225-0.0692-0.0601-0.06450.06750.04510.04660.07790.01950.01450.03170.03260.09625.8142-0.219629.0246
41.6573-0.27680.96471.9236-0.14610.56630.1819-0.0966-0.151-0.1964-0.10270.3270.1309-0.0565-0.07920.1556-0.0273-0.0070.03670.0250.16310.3868-2.279831.5919
50.2204-0.36140.11191.3731-0.25850.06910.01420.0106-0.03030.05220.02320.25980.0060.0154-0.03740.05430.00460.01750.05030.01890.101513.809312.122334.0541
60.5175-0.11161.40031.7807-0.15483.8036-0.08470.02010.06550.2239-0.0554-0.383-0.19350.04360.14010.0591-0.0072-0.03970.04390.04030.112132.311811.540838.244
70.7759-0.55340.37411.12580.07620.3445-0.0927-0.0198-0.08980.24640.01040.2790.0197-0.0150.08230.07690.00480.0480.05820.01390.11659.378718.21232.8938
85.0291-3.1017-0.17092.4202-0.14520.16-0.2419-0.0731-0.065-0.01780.1453-0.08180.0396-0.07210.09660.15180.0135-0.01440.0538-0.04870.070116.765927.17845.2129
92.38672.4677-0.00013.56010.00160.4022-0.00010.13890.0003-0.04650.0076-0.00330.02070.0359-0.00750.08990.0157-0.02190.06270.00120.019715.244437.74357.3626
100.13510.17930.2071.00110.02850.4773-0.0078-0.00560.03540.0127-0.00990.0366-0.0076-0.06210.01770.07490.02270.00560.06840.00130.060513.082746.058124.2752
110.70040.16690.36331.1246-0.20570.4437-0.05240.03720.1332-0.0775-0.0122-0.1119-0.0335-0.06110.06460.06760.01250.00910.04680.02170.07918.497351.083520.5796
120.42880.0442-0.06471.2361-0.09470.0480.0261-0.0426-0.03130.0765-0.0794-0.3067-0.0026-0.02910.05330.0605-0.0083-0.01450.0648-0.00340.104626.181740.14330.4283
130.81110.0493-0.27832.1953-0.19340.11110.0303-0.0295-0.06020.2998-0.05110.1827-0.02190.01760.02090.10010.00580.05650.0629-0.01110.04429.525935.831235.0762
141.21671.8537-0.86766.5849-1.40930.6236-0.0631-0.0712-0.00530.120.0259-0.49180.05250.04960.03720.03210.0085-0.01510.03830.02270.155134.861631.802530.1268
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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