PDB-6bq4: Crystal structure of Medicago truncatula Thermospermine Synthase ...

ID or keywords:

Entry

Database: PDB / ID: 6bq4

Title

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

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
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 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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Validation report

Summary document	6bq4_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	6bq4_full_validation.pdf.gz	1.3 MB	Display
Data in XML	6bq4_validation.xml.gz	24.4 KB	Display
Data in CIF	6bq4_validation.cif.gz	34.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/6bq4 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/6bq4	HTTPS FTP

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Related structure data

Related structure data	6bq2SC 6bq3C 6bq5C 6bq6C 6bq7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6bq5-1 6bq7-1 6bq3-1 6bq6-1 6bq2-1 2cmh-1 1bi8-d 6fi8-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
Related items in Molecule of the Month	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: Thermospermine synthase ACAULIS protein

B: Thermospermine synthase ACAULIS protein

hetero molecules

75.8 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)	81.040, 81.040, 163.800
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-594- HOH

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 186 molecules

#2: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#3: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.82 Å³/Da / Density % sol: 32.3 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG3350, 0.1 M Magnesium Chloride, 0.1 M MES buffer; cryo: 25% glycerol, Bis-Tris propane pH 6.5, 10% PEG3350, 0.1 M Magnesium Chloride

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 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: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.89→46.95 Å / Num. obs: 44135 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / R_merge(I) obs: 0.067 / Net I/σ(I): 23.9
Reflection shell	Resolution: 1.89→2.01 Å / Redundancy: 13 % / R_merge(I) obs: 1.268 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6935 / % possible all: 98.9

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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: 1.89→46.95 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.942 / SU B: 9.734 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23546	1016	2.3 %	RANDOM
R_work	0.18686	-	-	-
obs	0.18797	43117	99.78 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 43.123 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	0 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: 1 / Resolution: 1.89→46.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4672	0	81	180	4933

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	4893
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4497
X-RAY DIFFRACTION	r_angle_refined_deg	1.793	1.925	6634
X-RAY DIFFRACTION	r_angle_other_deg	1.025	3	10466
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.155	5	589
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.664	24.643	224
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.958	15	838
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.704	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	737
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5365
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	981
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	1.798	3.08	2356
X-RAY DIFFRACTION	r_mcbond_other	1.798	3.079	2355
X-RAY DIFFRACTION	r_mcangle_it	2.755	4.609	2945
X-RAY DIFFRACTION	r_mcangle_other	2.754	4.61	2946
X-RAY DIFFRACTION	r_scbond_it	2.278	3.41	2537
X-RAY DIFFRACTION	r_scbond_other	2.278	3.41	2537
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.572	4.985	3690
X-RAY DIFFRACTION	r_long_range_B_refined	5.701	36.416	5484
X-RAY DIFFRACTION	r_long_range_B_other	5.7	36.427	5485
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.895→1.944 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	72	-
R_work	0.366	3059	-
obs	-	-	97.54 %

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	2.4008	-1.3611	0.9807	1.8617	0.2683	1.0962	-0.0395	0.046	0.0304	-0.1582	-0.1611	0.1902	-0.0454	0.0545	0.2006	0.1412	0.1727	0.0318	0.2229	0.0656	0.0759	24.87	16.9481	6.9246
2	0.5891	1.4681	-0.1895	3.9849	-0.8364	0.9503	0.0531	0.0374	0.0985	0.0143	-0.1408	0.1648	0.1695	0.1139	0.0877	0.0883	0.0906	0.044	0.2019	0.0409	0.0669	26.7832	7.238	12.2074
3	0.161	0.1228	-0.095	0.3764	-0.2632	0.7308	0.0251	0.0004	0.014	0.0407	-0.1115	0.0364	0.0895	0.1661	0.0865	0.1228	0.0675	0.0436	0.0932	0.0193	0.124	27.999	3.84	30.5925
4	0.5307	0.0166	-0.3602	0.8943	0.1819	0.4246	-0.0653	0.0401	-0.009	0.0652	-0.0503	0.104	0.2011	0.044	0.1156	0.1681	0.0794	0.07	0.057	0.0338	0.1343	22.9011	-2.2543	27.9061
5	0.569	0.0099	0.0755	0.8983	-0.4002	0.3263	0.0523	0.0521	0.0542	0.0997	-0.0008	0.3138	0.0398	0.071	-0.0516	0.0861	0.0244	0.0907	0.0471	0.0181	0.2102	14.0996	10.1238	34.2153
6	0.554	0.047	0.337	1.7907	-1.0131	0.8147	0.1149	0.0155	0.1208	0.2942	-0.2128	-0.0032	-0.11	0.1481	0.0979	0.1145	-0.0175	0.0078	0.1253	0.0172	0.0947	29.9546	16.9056	38.5666
7	0.317	0.2749	0.4131	4.699	-1.4142	1.3095	-0.1185	0.1228	-0.2064	0.4472	0.6563	0.4258	-0.3384	-0.0777	-0.5378	0.1056	0.0244	0.1442	0.1281	0.0252	0.316	5.0915	17.3847	31.0474
8	3.1075	-2.1447	0.6378	2.0838	-1.4369	1.7979	-0.1848	0.1082	-0.0235	0.0603	-0.1288	-0.1414	0.0371	0.0952	0.3136	0.1299	0.0905	-0.0752	0.0928	-0.0455	0.1607	18.4847	27.5023	5.131
9	1.6673	2.1322	0.0981	5.244	0.5758	0.0916	0.0705	0.0435	-0.1142	-0.214	-0.1065	0.0177	-0.0569	-0.0051	0.036	0.1164	0.0072	-0.0419	0.1093	0.0229	0.0839	15.4723	38.7384	7.1112
10	0.2838	-0.0416	0.0185	0.5288	0.3931	0.8676	0.0192	0.0172	0.0313	0.0182	-0.0486	0.1781	-0.0819	0.0131	0.0293	0.0868	-0.0209	0.0049	0.0521	-0.0055	0.1769	12.5958	48.6867	22.0151
11	1.1466	0.0136	-0.6888	1.9729	0.0234	0.603	-0.019	-0.1032	0.0469	-0.1598	-0.0564	-0.0024	-0.1266	0.1924	0.0754	0.1373	-0.1165	-0.0379	0.1331	0.0269	0.11	27.8642	52.0481	25.0699
12	0.6143	-0.005	-0.1057	1.0766	0.1902	0.1118	0.049	-0.0447	-0.0707	0.1063	-0.099	-0.0429	-0.0079	0.0759	0.05	0.0689	-0.0525	-0.0007	0.1562	0.0322	0.1179	24.3201	38.9443	31.3322
13	0.7765	-0.9263	-1.7756	3.854	1.0295	4.4939	-0.1733	-0.0032	-0.1915	0.494	-0.0544	0.75	0.2752	0.0411	0.2277	0.078	-0.0265	0.1036	0.0492	-0.0175	0.2503	5.5553	38.9581	32.8115
14	0.1544	-0.1564	-0.1508	0.9787	0.9251	0.8753	-0.096	0.0301	0.0898	0.2841	0.1475	-0.0474	0.2671	0.1464	-0.0515	0.111	0.0106	-0.0231	0.1099	0.0428	0.1333	29.1878	33.2745	32.2318

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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