PDB-2o0l: Human spermidine synthase

ID or keywords:

Entry

Database: PDB / ID: 2o0l

Title

Human spermidine synthase

Components

Spermidine synthase

Keywords

TRANSFERASE / Spermidine Synthase / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

Metabolism of polyamines / polyamine metabolic process / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cellular response to leukemia inhibitory factor / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Min, J. / Wu, H. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)

Citation

Journal: Biochemistry / Year: 2007
Title: Structure and mechanism of spermidine synthases.
Authors: Wu, H. / Min, J. / Ikeguchi, Y. / Zeng, H. / Dong, A. / Loppnau, P. / Pegg, A.E. / Plotnikov, A.N.

History

Deposition	Nov 27, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2o0l.cif.gz	131.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2o0l.ent.gz	103.7 KB	Display	PDB format
PDBx/mmJSON format	2o0l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/2o0l ftp://data.pdbj.org/pub/pdb/validation_reports/o0/2o0l	HTTPS FTP

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Related structure data

Related structure data	2o05C 2o06C 2o07C C: citing same article (ref.)
Similar structure data	2o05-d 4yv2-d 4yv1-1 4yuw-d 2o07-d 6drh-3 4yuy-d 5b1s-2 2o57-2 4yuz-2 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: Spermidine synthase

B: Spermidine synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	58.323, 60.593, 86.667
Angle α, β, γ (deg.)	90.00, 108.96, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Spermidine synthase / Putrescine aminopropyltransferase / SPDSY Mass: 34001.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SRM, SPS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19623, spermidine synthase
#2: Chemical	ChemComp-S4M / 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE Mass: 356.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₄N₆O₃S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.13 Å³/Da / Density % sol: 42.21 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.2M Mg(OAc)2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
Detector	Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 13, 2006
Radiation	Monochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 1.99→81.92 Å / Num. all: 36969 / Num. obs: 36969 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / R_merge(I) obs: 0.121 / Net I/σ(I): 7.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
CrystalClear	(MSC/RIGAKU)	data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→81.92 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.906 / SU B: 8.898 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.216 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26755	1945	5 %	RANDOM
R_work	0.2062	-	-	-
all	0.20923	36969	-	-
obs	0.20923	36969	98.63 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 21.46 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.25 Å²	0 Å²	-0.33 Å²
2-	-	-0.38 Å²	0 Å²
3-	-	-	-1.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→81.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4443	0	48	265	4756

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	4596
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.521	1.971	6225
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.787	5	556
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.311	24.608	217
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.717	15	787
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.166	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	681
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3483
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	2172
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	3050
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	324
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	0.182	0.2	55
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.211	0.2	11
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	0.718	1.5	2904
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.079	2	4511
X-RAY DIFFRACTION	r_scbond_it	2.041	3	1977
X-RAY DIFFRACTION	r_scangle_it	2.922	4.5	1714
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.99→2.04 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.338	124	-
R_work	0.285	2445	-
obs	-	-	89.48 %

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	0.8158	0.7268	-0.7987	2.1675	-1.8995	6.063	0.0316	-0.0523	0.138	0.1496	0.1361	0.275	-0.017	-0.407	-0.1677	0.0078	0.013	0.0153	0.1084	-0.0281	0.0972	13.3168	21.7112	67.3151
2	3.0368	0.2886	-1.7095	6.1781	-1.4576	1.2351	0.1772	-0.1315	0.3747	0.463	0.0781	0.4471	-0.2571	0.043	-0.2553	0.0936	-0.0266	0.0696	0.0948	-0.0166	0.0429	16.542	28.4169	81.085
3	2.1143	-0.5005	0.4086	0.1187	-0.079	1.3448	-0.015	0.0536	0.1127	0.01	0.029	0.034	0.0542	-0.167	-0.014	0.0759	-0.005	0.0331	0.0935	-0.0128	0.0338	21.1096	21.4648	75.2062
4	3.6703	1.8389	-1.4604	2.5365	-1.3155	1.3012	0.1228	-0.0406	0.0422	0.2289	-0.071	-0.0187	-0.1087	0.0652	-0.0518	0.0752	0.0091	-0.0025	0.0812	-0.0041	0.0494	38.8991	24.7276	69.356
5	1.8921	-0.3482	-0.8599	2.667	-0.4551	1.8813	0.1645	-0.1403	0.0162	0.272	-0.1481	-0.2196	-0.1222	0.1465	-0.0164	0.1108	-0.0168	-0.0241	0.0808	0.0048	0.0336	42.4313	31.6555	76.2371
6	2.3225	1.0103	-0.5059	2.2283	-1.3862	0.8705	0.2829	-0.3169	0.0927	0.3417	-0.2218	-0.0338	-0.1368	-0.0206	-0.0611	0.1527	-0.059	0.022	0.0901	-0.0254	-0.017	29.7771	30.2195	83.2871
7	2.1772	-0.2859	0.4063	2.1458	0.5922	0.9434	0.1302	-0.0868	0.1071	0.1537	-0.0675	0.1036	-0.097	-0.0936	-0.0627	0.0907	-0.0179	0.0383	0.0466	-0.022	0.0414	37.6358	41.6742	74.3586
8	7.2186	-2.2361	-0.5932	5.3063	0.5379	4.2792	0.0357	0.153	0.0547	-0.1017	0.0019	0.0906	-0.2131	0.0104	-0.0376	0.0936	-0.0157	0.0326	0.0437	0.0043	0.0646	40.66	43.8041	64.4324
9	3.2276	1.3592	1.1631	0.5815	0.5887	1.4907	0.0151	-0.0064	0.2589	0.1564	-0.0364	0.0859	-0.0042	-0.1016	0.0213	0.016	0.0172	0.0129	0.0663	-0.0021	0.1124	28.6608	30.7312	56.4899
10	31.7525	12.278	4.9307	12.861	2.3617	11.6579	0.0364	0.4775	-0.0364	-0.2221	0.1283	0.4164	0.0411	-0.0518	-0.1646	0.0679	0.0592	0.0113	0.0193	0.032	0.0541	34.313	39.4319	52.9017
11	1.5142	1.6864	-0.3902	2.9701	-0.6182	0.1583	0.082	-0.0317	-0.0318	0.1087	-0.1008	-0.0349	-0.0593	0.0412	0.0188	0.0541	0.0021	0.0062	0.0772	-0.0066	0.044	33.1993	28.1866	60.0114
12	1.0984	-1.0464	-0.0114	2.6087	0.235	2.9606	0.0531	0.0419	-0.1952	-0.2536	0.0673	-0.1098	0.1065	0.0445	-0.1204	0.0618	0.0121	0.0165	0.0531	-0.0003	0.0987	46.7722	32.8188	58.5246
13	5.5175	3.8789	-5.0652	7.6161	-2.1753	5.0428	-0.0254	-0.3252	-0.1467	0.4538	-0.1925	-0.4474	-0.1687	0.3586	0.2179	0.0577	0.0016	-0.066	0.1085	0.0437	0.0656	48.65	17.8429	71.5007
14	2.09	-0.5572	2.5125	0.6372	-1.3458	5.53	-0.0534	0.0437	-0.016	0.0031	-0.0066	-0.0455	0.0729	0.0881	0.06	0.0534	-0.0043	0.0113	0.0573	-0.0062	0.1023	39.4489	20.6765	58.0684
15	14.5993	4.5749	-5.9887	10.0703	0.8543	15.0278	-0.1969	0.1563	0.5053	-0.9725	0.0952	-0.0139	-0.878	0.1321	0.1017	0.0706	-0.014	0.0017	-0.0039	0.0331	0.0627	34.7923	28.9566	44.6893
16	15.7266	8.7037	-10.1211	13.6645	2.0339	24.1305	-0.4654	-0.5668	-0.9743	1.5743	0.227	-0.531	1.3853	-1.6875	0.2384	0.0456	-0.0595	-0.0058	0.1526	0.0039	0.0701	4.1973	16.8907	61.4257
17	3.4309	-0.7849	1.8472	0.605	-0.1159	1.2157	-0.0062	-0.0736	-0.1788	0.0882	-0.0024	0.1054	0.0383	-0.0724	0.0085	0.0326	-0.0028	0.0447	0.0999	-0.0151	0.0585	13.2875	12.6087	62.2916
18	1.8513	4.7207	2.1019	30.777	-3.8031	6.8663	0.1886	0.0057	-0.3308	-0.1364	-0.2157	1.2043	0.2602	-0.0717	0.0271	-0.0691	0.0244	0.0303	0.111	0.0029	0.1751	2.6002	8.0915	49.6763
19	2.4381	0.8295	-0.084	0.9507	-0.3687	0.9896	-0.0857	0.0443	-0.1797	-0.0268	0.0053	0.0761	0.0278	-0.0804	0.0804	0.0271	0.0005	0.007	0.0861	-0.0249	0.0756	12.5414	10.7078	50.7637
20	0.6321	0.3996	-0.0531	1.0371	0.0863	1.4668	-0.0022	0.0487	-0.0974	-0.1104	0.0002	0.0269	-0.0357	0.0219	0.002	0.0348	0.0055	-0.0005	0.0648	-0.0092	0.0813	29.3002	4.1721	40.0169
21	2.1026	-1.5835	-0.7818	3.5173	-0.9153	1.3863	0.1371	0.1737	-0.3075	-0.1737	-0.1113	0.1929	-0.0594	-0.1953	-0.0257	0.0163	0.0122	-0.0465	0.0693	-0.0427	0.0901	12.4041	5.5249	40.8162
22	1.4714	0.2517	-0.169	3.4664	-0.3621	1.85	0.052	-0.039	-0.1333	0.1922	-0.0679	0.1826	0.0326	-0.15	0.0159	0.0309	-0.0128	0.016	0.056	-0.0134	0.0948	24.9628	-5.8984	42.5017
23	0.3262	-1.6772	1.497	9.0167	-5.25	22.093	0.0162	-1.327	-0.0349	1.0521	-0.1238	0.1579	0.6304	0.4646	0.1076	0.0632	0.0601	0.0497	0.0621	0.0521	0.1549	20.0062	-6.8362	56.1447
24	2.7824	-0.1341	0.6227	4.5166	-0.3301	2.7434	-0.044	-0.1542	-0.0407	0.265	0.129	0.1197	0.2132	-0.0688	-0.085	0.0487	0.0054	-0.0003	0.0817	0.0134	0.1055	33.4303	-7.0147	48.388
25	5.7333	-5.7512	-0.9769	9.9549	2.1947	3.0352	-0.1057	-0.0651	-0.4907	0.3556	-0.137	0.3043	0.1745	-0.0361	0.2427	0.0635	-0.0226	0.029	0.0657	0.0072	0.0508	30.78	3.6973	64.4593
26	7.6388	-6.1247	-5.8586	12.067	4.755	16.2261	0.1315	-0.4327	0.0292	0.0654	0.0679	-0.1525	0.0478	0.2585	-0.1994	0.0175	-0.0045	-0.0067	0.0676	0.0277	0.0653	38.827	-6.3105	57.7113
27	1.6582	-1.7557	-0.1295	2.4421	0.2436	0.0296	0.1002	-0.0482	-0.0608	-0.128	-0.0908	0.0356	-0.0171	0.021	-0.0095	0.0486	0.013	-0.0076	0.0863	0.0024	0.0427	30.2129	9.1792	56.0106
28	0.1159	0.1983	0.4153	2.0379	-0.3583	2.1613	0.0602	0.0108	0.0442	0.1604	0.0107	-0.2269	-0.2418	0.0375	-0.071	0.0329	0.004	0.0024	0.0636	0.0034	0.1159	42.8022	1.9468	48.1231
29	0.3745	0.0449	0.2979	1.7323	-0.7992	3.4084	0.0763	0.108	0.0228	-0.2139	-0.0282	-0.0409	0.0313	0.131	-0.0481	0.0632	-0.0032	0.0245	0.0754	-0.0095	0.0912	36.7263	15.6729	43.5317
30	10.4521	1.1702	3.742	10.0728	5.4585	8.6493	-0.0664	-0.262	-0.5524	0.2157	0.0046	-0.2528	0.6795	0.2429	0.0618	0.0736	0.0223	0.0153	0.0328	0.0182	0.0718	40.4927	8.4122	66.1856

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	16 - 36	18 - 38
2	X-RAY DIFFRACTION	2	A	A	37 - 54	39 - 56
3	X-RAY DIFFRACTION	3	A	A	55 - 72	57 - 74
4	X-RAY DIFFRACTION	4	A	A	73 - 93	75 - 95
5	X-RAY DIFFRACTION	5	A	A	94 - 121	96 - 123
6	X-RAY DIFFRACTION	6	A	A	122 - 146	124 - 148
7	X-RAY DIFFRACTION	7	A	A	147 - 175	149 - 177
8	X-RAY DIFFRACTION	8	A	A	187 - 202	189 - 204
9	X-RAY DIFFRACTION	9	A	A	203 - 218	205 - 220
10	X-RAY DIFFRACTION	10	A	A	219 - 225	221 - 227
11	X-RAY DIFFRACTION	11	A	A	226 - 248	228 - 250
12	X-RAY DIFFRACTION	12	A	A	249 - 263	251 - 265
13	X-RAY DIFFRACTION	13	A	A	264 - 276	266 - 278
14	X-RAY DIFFRACTION	14	A	A	277 - 294	279 - 296
15	X-RAY DIFFRACTION	15	A	A	295 - 300	297 - 302
16	X-RAY DIFFRACTION	16	B	B	15 - 20	17 - 22
17	X-RAY DIFFRACTION	17	B	B	21 - 38	23 - 40
18	X-RAY DIFFRACTION	18	B	B	39 - 45	41 - 47
19	X-RAY DIFFRACTION	19	B	B	46 - 77	48 - 79
20	X-RAY DIFFRACTION	20	B	B	78 - 124	80 - 126
21	X-RAY DIFFRACTION	21	B	B	125 - 144	127 - 146
22	X-RAY DIFFRACTION	22	B	B	145 - 177	147 - 179
23	X-RAY DIFFRACTION	23	B	B	178 - 186	180 - 188
24	X-RAY DIFFRACTION	24	B	B	187 - 207	189 - 209
25	X-RAY DIFFRACTION	25	B	B	208 - 220	210 - 222
26	X-RAY DIFFRACTION	26	B	B	221 - 228	223 - 230
27	X-RAY DIFFRACTION	27	B	B	229 - 248	231 - 250
28	X-RAY DIFFRACTION	28	B	B	249 - 263	251 - 265
29	X-RAY DIFFRACTION	29	B	B	264 - 290	266 - 292
30	X-RAY DIFFRACTION	30	B	B	291 - 299	293 - 301

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