PDB-6bq6: Crystal structure of Medicago truncatula Thermospermine Synthase ...

ID or keywords:

Entry

Database: PDB / ID: 6bq6

Title

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with thermospermine

Components

Thermospermine synthase

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
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 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	6bq6.cif.gz	251 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6bq6_validation.pdf.gz	441.1 KB	Display	wwPDB validaton report
Full document	6bq6_full_validation.pdf.gz	442.3 KB	Display
Data in XML	6bq6_validation.xml.gz	25.5 KB	Display
Data in CIF	6bq6_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/6bq6 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/6bq6	HTTPS FTP

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Related structure data

Related structure data	6bq2SC 6bq3C 6bq4C 6bq5C 6bq7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6bq2-1 6bq4-1 6bq7-1 6bq5-1 2cmh-1 6bq3-1 1ofp-d 1iy9-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

B: Thermospermine synthase

hetero molecules

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

1

A: Thermospermine synthase

B: Thermospermine synthase

hetero molecules

A: Thermospermine synthase

B: Thermospermine synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.293, 80.293, 163.245
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-681- HOH

#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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-TER / N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE / THERMOSPERMINE / PA(334) Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₆N₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 341 / 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: 1.76 Å³/Da / Density % sol: 30.29 %
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 33% PEG400

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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: 1.65→46.61 Å / Num. obs: 65012 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / R_merge(I) obs: 0.068 / Net I/σ(I): 23.5
Reflection shell	Resolution: 1.65→1.75 Å / Redundancy: 12.8 % / R_merge(I) obs: 1.287 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10267 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	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: 1.65→46.61 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.93 / SU B: 5.201 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23027	1041	1.6 %	RANDOM
R_work	0.17211	-	-	-
obs	0.17303	63970	99.84 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 29.913 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	0 Å²	0 Å²
2-	-	-0.12 Å²	0 Å²
3-	-	-	0.25 Å²

Refinement step

Cycle: 1 / Resolution: 1.65→46.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4663	0	30	341	5034

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	4891
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4626
X-RAY DIFFRACTION	r_angle_refined_deg	1.681	1.954	6626
X-RAY DIFFRACTION	r_angle_other_deg	0.997	3	10700
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.932	5	599
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.598	24.693	228
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.674	15	847
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	26.82	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	729
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5509
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1101
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	1.48	2.24	2384
X-RAY DIFFRACTION	r_mcbond_other	1.479	2.239	2383
X-RAY DIFFRACTION	r_mcangle_it	2.403	3.35	2987
X-RAY DIFFRACTION	r_mcangle_other	2.403	3.352	2988
X-RAY DIFFRACTION	r_scbond_it	1.888	2.521	2507
X-RAY DIFFRACTION	r_scbond_other	1.887	2.522	2508
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.102	3.66	3639
X-RAY DIFFRACTION	r_long_range_B_refined	5.524	18.653	5643
X-RAY DIFFRACTION	r_long_range_B_other	5.523	18.658	5644
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.649→1.692 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.303	74	-
R_work	0.288	4527	-
obs	-	-	98.04 %

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	3.2196	-1.4566	-0.7487	1.5357	-0.0477	0.4251	-0.1365	0.0357	0.0501	-0.0751	0.0606	0.0112	0.1379	-0.0195	0.0759	0.0593	0.015	0.0422	0.0505	0.0201	0.1232	23.2488	16.3786	6.6195
2	1.2834	0.7608	0.0985	3.0467	-1.5737	1.0388	0.0359	0.0904	0.0289	-0.1762	0.0106	0.1091	0.1513	0.032	-0.0465	0.126	0.0023	0.0478	0.0122	-0.0013	0.0305	25.6187	5.6836	11.2138
3	0.0042	-0.0357	0.0416	0.883	-0.5553	0.7399	0.0002	-0.0001	-0.0051	-0.1007	-0.0908	-0.1054	0.0731	0.0454	0.0906	0.0586	0.023	0.0291	0.016	0.0272	0.0775	25.7198	-0.2304	28.7057
4	1.227	-0.5268	0.8572	1.0147	-0.0967	0.7039	0.1415	-0.0468	-0.1558	-0.1287	-0.083	0.177	0.1084	-0.0685	-0.0585	0.1103	-0.0131	-0.0122	0.0236	0.0104	0.1059	10.1024	-1.7575	30.3207
5	0.2724	-0.0952	0.19	0.9458	-0.2608	0.1748	0.0068	0.0116	-0.0083	0.0292	0.0212	0.1194	0.0033	0.005	-0.028	0.045	0.0005	0.0119	0.0202	0.0076	0.0685	13.7692	12.0073	33.7629
6	0.413	-0.3811	1.1164	2.8241	-0.6934	3.0644	-0.0879	0.0108	0.093	0.234	-0.1183	-0.4574	-0.2161	0.0163	0.2062	0.0303	-0.0047	-0.0323	0.0147	0.0405	0.1293	32.1903	11.4118	37.9645
7	0.734	-0.2714	0.4537	0.6441	-0.0521	0.3077	0.0241	0.0226	-0.0008	0.1575	-0.0626	0.1309	0.043	0	0.0385	0.0671	-0.009	0.0184	0.0191	-0.0089	0.0828	9.6913	18.8982	32.9366
8	1.8863	-1.5253	-0.2487	1.6839	-0.2233	0.4414	-0.15	-0.0434	0.0554	0.0649	0.0623	-0.1264	0.0478	-0.0388	0.0877	0.0761	0.0418	-0.0475	0.0361	-0.0439	0.0653	16.9121	27.1266	5.1624
9	1.7951	2.3225	-0.2948	4.2317	-0.2682	0.4122	0.0289	0.067	-0.0533	-0.0263	-0.0455	-0.0256	-0.0121	0.0125	0.0165	0.0701	0.0167	-0.025	0.0239	-0.0056	0.016	15.3957	37.6428	7.2722
10	0.1633	0.2033	0.2434	0.7742	0.1521	0.4088	-0.0016	-0.0161	0.0292	0.0001	-0.0263	0.0823	0.0019	-0.0288	0.0279	0.0479	0.0126	0.0121	0.0346	-0.0061	0.0555	13.1081	45.8943	24.1231
11	0.4049	0.3046	0.0577	0.8281	-0.0484	0.5098	-0.0494	0.0296	0.0621	-0.0624	0.0066	-0.033	-0.0779	-0.0073	0.0428	0.0476	0.0068	0.0107	0.0083	0.0067	0.0613	18.6937	50.9727	20.451
12	0.3019	0.1858	-0.0722	0.9097	0.1161	0.1024	0.0307	-0.0257	-0.0381	0.0534	-0.0496	-0.1744	0.0039	-0.021	0.0189	0.0419	-0.0097	-0.0077	0.0232	0.0041	0.0727	26.2089	39.9354	30.2183
13	0.5477	0.1793	-0.2026	2.2655	-0.0965	0.0758	0.1198	-0.0462	-0.0416	0.2709	-0.1358	0.2416	-0.0431	0.0207	0.016	0.0924	-0.0132	0.0537	0.0253	-0.0093	0.0667	9.5951	35.6529	34.9311
14	1.1405	1.7212	-0.5767	5.1076	-1.0318	0.3051	-0.0445	-0.0318	-0.0298	0.1044	0.0243	-0.333	0.0156	0.0124	0.0202	0.0291	0.0082	-0.0208	0.0197	0.0017	0.1203	34.9056	31.6066	29.996

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 46
2	X-RAY DIFFRACTION	2	A	47 - 76
3	X-RAY DIFFRACTION	3	A	77 - 167
4	X-RAY DIFFRACTION	4	A	168 - 205
5	X-RAY DIFFRACTION	5	A	206 - 275
6	X-RAY DIFFRACTION	6	A	276 - 287
7	X-RAY DIFFRACTION	7	A	288 - 314
8	X-RAY DIFFRACTION	8	B	24 - 47
9	X-RAY DIFFRACTION	9	B	48 - 76
10	X-RAY DIFFRACTION	10	B	77 - 140
11	X-RAY DIFFRACTION	11	B	141 - 189
12	X-RAY DIFFRACTION	12	B	190 - 274
13	X-RAY DIFFRACTION	13	B	275 - 297
14	X-RAY DIFFRACTION	14	B	298 - 315

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