PDB-6bq5: Crystal structure of Medicago truncatula Thermospermine Synthase ...

ID or keywords:

Entry

Database: PDB / ID: 6bq5

Title

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with 5'-methylthioadenosine

Components

Thermospermine synthase ACAULIS protein

Keywords

TRANSFERASE / polyamine biosynthesis / tetraamine /

thermospermine /

spermidine / aminopropyl transferase

Function / homology

Function and homology information

thermospermine synthase activity /

spermidine synthase /

spermidine synthase activity / polyamine biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Sekula, B. / Dauter, Z.

Funding support

United States, 1items

Citation

Journal: Biochem. J. / Year: 2018
Title: Crystal structure of thermospermine synthase fromMedicago truncatulaand substrate discriminatory features of plant aminopropyltransferases.
Authors: Sekula, B. / Dauter, Z.

History

Deposition	Nov 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 7, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	May 2, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3	Mar 23, 2022	Group: 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 1.4	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6bq5.cif.gz	254.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/6bq5 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/6bq5	HTTPS FTP

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Related structure data

Related structure data	6bq2SC 6bq3C 6bq4C 6bq6C 6bq7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6bq4-1 6bq7-1 6bq3-1 6bq6-1 6fi8-d 2cmh-1 6bq2-1 1bi8-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thermospermine synthase ACAULIS protein

B: Thermospermine synthase ACAULIS protein

hetero molecules

76 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
Evidence: SAXS, gel filtration
152 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.766, 82.766, 164.194
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-659- HOH

#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-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#3: Chemical	ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.89 Å³/Da / Density % sol: 34.77 %
Crystal grow	Temperature: 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 25% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.8→47.66 Å / Num. obs: 53857 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / R_merge(I) obs: 0.062 / Net I/σ(I): 22.2
Reflection shell	Resolution: 1.8→1.91 Å / Redundancy: 8.6 % / R_merge(I) obs: 1.049 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8457 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
XDS	May 1, 2016	data reduction
XSCALE	Nov 1, 2016	data scaling
PHASER	2.5.6	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6BQ2

6bq2

Resolution: 1.8→47.66 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.953 / SU B: 7.212 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21608	1078	2 %	RANDOM
R_work	0.17565	-	-	-
obs	0.17646	52775	99.81 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 37.003 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.19 Å²	0 Å²	0 Å²
2-	-	-0.19 Å²	0 Å²
3-	-	-	0.37 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→47.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4672	0	96	317	5085

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	4914
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4522
X-RAY DIFFRACTION	r_angle_refined_deg	1.69	1.928	6659
X-RAY DIFFRACTION	r_angle_other_deg	1.015	3	10526
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.789	5	590
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.67	24.69	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.58	15	844
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.351	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	738
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5379
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	983
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.146	1.809	2354
X-RAY DIFFRACTION	r_mcbond_other	1.143	1.808	2353
X-RAY DIFFRACTION	r_mcangle_it	1.912	2.704	2943
X-RAY DIFFRACTION	r_mcangle_other	1.911	2.705	2944
X-RAY DIFFRACTION	r_scbond_it	1.533	2.086	2560
X-RAY DIFFRACTION	r_scbond_other	1.533	2.086	2560
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.491	3.025	3716
X-RAY DIFFRACTION	r_long_range_B_refined	5.879	22.443	5570
X-RAY DIFFRACTION	r_long_range_B_other	5.879	22.451	5571
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.797→1.843 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	77	-
R_work	0.341	3745	-
obs	-	-	98.05 %

Refinement TLS params.

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

ID	L11 (°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)
1	3.0585	-1.9067	0.2588	1.3874	0.4473	2.1339	-0.0277	-0.0304	0.0395	-0.0237	0.0586	0.018	0.0743	0.2105	-0.0309	0.1767	0.052	-0.0068	0.2251	0.0189	0.1955	26.1388	18.1172	7.0427
2	1.4073	1.4828	-0.3195	3.9941	-0.2832	0.6177	0.0419	0.2356	0.2215	0.0612	0.1691	0.1751	0.3385	0.2828	-0.2111	0.2791	0.1837	-0.0484	0.3037	-0.0721	0.1349	27.8781	8.5113	12.2714
3	0.1721	0.1556	0.104	0.1651	-0.1236	2.3713	0.1029	0.0094	0.1149	0.0368	-0.0036	0.1266	0.4861	0.5647	-0.0993	0.2801	0.2111	-0.0382	0.2659	-0.0481	0.1236	29.2591	5.1967	30.5581
4	1.6312	-0.1611	-1.0722	1.5897	0.5744	1.1969	-0.2265	0.108	0.0196	0.0804	0.1596	0.2637	0.7101	0.2419	0.0669	0.7979	0.3889	-0.0618	0.2331	-0.0141	0.0511	24.2652	-0.8913	27.8835
5	0.2164	-0.062	-0.041	0.4138	-0.2081	0.8954	0.0217	0.0334	0.0197	-0.0041	0.0674	0.1863	0.2391	0.0975	-0.0892	0.1979	0.0285	-0.0122	0.1353	-0.0005	0.2098	15.2451	11.1573	34.2762
6	0.8823	-0.0391	1.2346	0.3307	-0.3162	1.9519	0.0732	0.1444	0.045	0.1341	-0.0703	0.1114	-0.0201	0.3243	-0.0028	0.138	0.0402	-0.0291	0.301	-0.027	0.1379	31.0483	18.2739	38.6451
7	0.8227	1.3472	-0.2217	4.7886	0.4298	0.9423	0.1397	0.0543	-0.0981	0.1905	0.0107	0.1285	-0.0515	-0.3105	-0.1504	0.0826	-0.023	-0.0317	0.205	0.0476	0.2782	6.0348	18.3104	31.246
8	3.2906	-2.2485	1.9177	1.6026	-1.5053	2.7368	0.0155	-0.0356	0.0751	-0.1021	-0.0248	-0.0781	-0.1294	0.0954	0.0093	0.2477	0.029	-0.0017	0.1626	-0.0557	0.1867	19.4534	28.6895	5.092
9	2.1308	2.2092	-0.1305	4.177	0.1241	0.0542	-0.0956	0.1018	-0.0241	-0.2547	0.0369	0.0683	-0.0274	-0.006	0.0587	0.1921	-0.0174	-0.0429	0.1716	0.0069	0.1665	16.096	40.016	7.017
10	0.2971	-0.1512	0.0626	0.2653	0.0815	1.0297	-0.0986	0.027	0.0002	0.0453	0.059	0.0584	-0.1642	-0.0896	0.0396	0.1926	0.0079	-0.0343	0.1671	0.0054	0.1706	12.8582	49.7496	22.0401
11	1.0659	-0.335	-0.5001	1.0189	0.4579	1.4668	-0.1002	0.0672	0.1411	-0.1595	0.0283	-0.0201	-0.3346	0.1616	0.0719	0.2241	-0.0731	-0.0311	0.1611	0.0061	0.1683	28.0966	53.4614	25.2021
12	0.2904	-0.0465	0.2265	0.7123	0.0148	0.2102	-0.0483	0.0537	-0.0403	0.0839	0.0319	-0.0476	-0.0584	0.1014	0.0163	0.1569	-0.0245	-0.0198	0.2123	-0.0042	0.1708	24.8395	40.3623	31.4632
13	0.9047	-0.884	-1.572	4.4123	0.6581	2.9509	-0.1403	0.113	-0.0574	0.3432	0.1312	0.3435	0.1683	-0.2457	0.0091	0.1043	0.0317	0.0298	0.228	0.0394	0.2153	6.094	39.776	32.9214
14	0.698	0.0308	0.2475	0.5662	0.0024	0.1608	-0.0215	0.003	-0.0481	0.2963	0.0569	-0.0403	-0.0286	0.1271	-0.0354	0.1643	-0.004	-0.0369	0.2338	-0.005	0.1556	29.824	34.7623	32.3653

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 47
2	X-RAY DIFFRACTION	2	A	48 - 76
3	X-RAY DIFFRACTION	3	A	77 - 140
4	X-RAY DIFFRACTION	4	A	141 - 189
5	X-RAY DIFFRACTION	5	A	190 - 274
6	X-RAY DIFFRACTION	6	A	275 - 297
7	X-RAY DIFFRACTION	7	A	298 - 315
8	X-RAY DIFFRACTION	8	B	24 - 46
9	X-RAY DIFFRACTION	9	B	47 - 76
10	X-RAY DIFFRACTION	10	B	77 - 167
11	X-RAY DIFFRACTION	11	B	168 - 205
12	X-RAY DIFFRACTION	12	B	206 - 275
13	X-RAY DIFFRACTION	13	B	276 - 287
14	X-RAY DIFFRACTION	14	B	288 - 315

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