PDB-4jly: Dodecameric structure of spermidine N-acetyltransferase from Vibr...

ID or keywords:

Entry

Database: PDB / ID: 4jly

Title

Dodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae

Components

Spermidine n1-acetyltransferase

Keywords

TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / spermidine / N-acetyltransferase

Function / homology

Function and homology information

polyamine catabolic process / spermine catabolic process / spermidine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar eltor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.882 Å

Authors

Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Kuhn, M.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: J.Mol.Biol. / Year: 2015
Title: Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG.
Authors: Filippova, E.V. / Weigand, S. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Anderson, W.F.

History

Deposition	Mar 13, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 7, 2015	Group: Database references
Revision 1.2	Nov 18, 2015	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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	4jly.cif.gz	443.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4jly.ent.gz	372.5 KB	Display	PDB format
PDBx/mmJSON format	4jly.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/jl/4jly ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jly	HTTPS FTP

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Related structure data

Related structure data	4ygoC 5cnpC 3eg7 PDB Unreleased entryS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ug4-1 4jjx-1 7kwx-1 7kx2-1 4ncz-1 7kx3-1 6cx8-1 3tth-13 4ygo-1 5ix3-1 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
Other databases	TargetTrack: CSGID-IDP01616

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: Spermidine n1-acetyltransferase

B: Spermidine n1-acetyltransferase

C: Spermidine n1-acetyltransferase

D: Spermidine n1-acetyltransferase

E: Spermidine n1-acetyltransferase

F: Spermidine n1-acetyltransferase

hetero molecules

126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Spermidine n1-acetyltransferase

B: Spermidine n1-acetyltransferase

C: Spermidine n1-acetyltransferase

D: Spermidine n1-acetyltransferase

E: Spermidine n1-acetyltransferase

F: Spermidine n1-acetyltransferase

hetero molecules

A: Spermidine n1-acetyltransferase

B: Spermidine n1-acetyltransferase

C: Spermidine n1-acetyltransferase

D: Spermidine n1-acetyltransferase

E: Spermidine n1-acetyltransferase

F: Spermidine n1-acetyltransferase

hetero molecules

defined by author&software
253 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	194.860, 71.771, 136.728
Angle α, β, γ (deg.)	90.00, 134.53, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Spermidine n1-acetyltransferase Mass: 20975.646 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9KL03
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.71 Å³/Da / Density % sol: 54.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M Ammonium Sulfate, 0.1 M tri-Sodium Citrate, 15 % PEG8000 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2011 / Details: MIRROR
Radiation	Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.88→30 Å / Num. all: 30456 / Num. obs: 30456 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 76.9 Å² / R_merge(I) obs: 0.076 / Net I/σ(I): 22.03
Reflection shell	Resolution: 2.88→2.95 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1452 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.7.0032	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EG7

3eg7
PDB Unreleased entry

Resolution: 2.882→28.91 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.908 / SU B: 39.397 / SU ML: 0.339 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27698	1532	5 %	RANDOM
R_work	0.18514	-	-	-
obs	0.18973	28867	98.99 %	-
all	-	28867	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 84.087 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.17 Å²	0 Å²	-1 Å²
2-	-	4.52 Å²	-0 Å²
3-	-	-	-0.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.882→28.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8655	0	25	30	8710

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	8897
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8360
X-RAY DIFFRACTION	r_angle_refined_deg	1.557	1.937	12017
X-RAY DIFFRACTION	r_angle_other_deg	0.829	3	19088
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.412	5	1021
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.753	23.955	536
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.965	15	1567
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.955	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1264
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10206
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2337
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.882→2.957 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.354	120	-
R_work	0.288	1942	-
obs	-	-	91.32 %

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	9.7168	3.1533	-6.0972	8.0812	-3.591	12.321	-0.0156	0.5407	1.1959	-0.2027	0.3267	0.1493	-0.9669	0.0858	-0.311	0.2955	0.0687	-0.1151	0.2331	0.0329	0.2438	-2.9198	36.7555	-25.9414
2	21.4762	-1.8895	-14.201	2.8417	5.1051	14.961	0.0705	0.4942	0.746	-0.6765	-0.187	0.4015	-0.9582	-0.5477	0.1165	0.4699	-0.0344	-0.2729	0.2936	-0.075	0.5273	-13.7836	26.0878	-25.1081
3	3.2494	-0.2259	-1.183	5.137	5.4305	6.0526	-0.0718	-0.3845	0.3104	0.0733	-0.1678	0.2747	0.1691	0.0076	0.2396	0.2979	0.1047	-0.014	0.3062	0.0375	0.1264	-2.3353	27.647	-25.351
4	3.0739	0.4891	0.1631	2.5474	-0.2991	1.6177	-0.1706	0.5477	0.8028	-0.1885	0.0743	0.155	-0.6311	-0.3188	0.0963	0.5059	0.0661	-0.068	0.2031	0.131	0.2122	-7.6714	26.3307	-40.7267
5	5.3667	0.3895	-13.7357	7.0647	-2.6319	35.5964	0.5191	0.2292	0.3476	-0.6806	0.1189	-0.4743	-1.0791	-0.5225	-0.638	0.4348	-0.1004	0.0538	0.3986	0.2561	0.3704	8.3744	25.0908	-49.9559
6	5.0882	1.3776	1.0459	8.5463	-1.5329	7.4049	0.2286	0.2918	0.2254	-0.1044	-0.0657	0.3045	-0.7504	-0.1281	-0.1629	0.1257	0.0482	0.0825	0.3005	-0.0228	0.3946	-24.2978	36.8803	-10.7405
7	1.7054	3.7547	-5.9136	8.3003	-13.0571	20.5493	0.6554	0.3607	0.4088	1.6013	0.7096	0.8565	-2.4518	-1.1483	-1.365	0.8096	0.1239	0.0286	0.8587	0.0805	0.7647	-33.435	30.2442	1.1751
8	8.6301	2.123	-0.3371	5.2298	-0.2099	5.0253	0.1702	-0.0876	-0.6634	0.2154	-0.4567	-0.6394	-0.0056	0.4531	0.2865	0.0909	-0.021	0.0671	0.2643	-0.0275	0.2776	-22.0665	28.7902	-7.0674
9	1.0274	0.9947	-0.5346	3.7853	-1.2399	2.017	-0.0461	0.2512	0.1462	-0.2954	0.2005	0.0494	-0.3706	-0.315	-0.1545	0.1675	0.0865	0.0122	0.2636	-0.0088	0.2802	-38.0475	25.4344	-14.0435
10	4.0219	9.3494	-1.9206	21.9949	-4.6773	1.0967	0.1014	-0.0791	0.5124	0.5258	-0.1659	0.8241	-0.2726	-0.0415	0.0645	0.699	0.0893	-0.0959	0.7555	-0.0019	0.8146	-39.0384	26.288	-30.3828
11	0.0183	0.2274	-0.2174	4.1435	-3.8332	3.5564	-0.095	0.0048	0.0769	-1.2379	0.6999	0.5737	1.1712	-0.6313	-0.6049	0.9466	-0.2023	-0.0013	0.7963	-0.0678	0.8592	-22.3099	-16.0027	-32.279
12	8.2521	2.4188	-2.3967	8.6733	-4.0951	5.9012	0.2523	0.2661	-0.1283	-0.0374	-0.317	-0.6187	-0.4404	0.1186	0.0647	0.3254	-0.0059	-0.0028	0.2545	-0.0395	0.1181	-5.5124	-0.9738	-22.8906
13	2.9955	-0.4696	0.3787	5.26	-0.7462	1.5598	-0.1542	0.0749	-0.4385	-0.0636	0.1654	0.4494	0.22	-0.0767	-0.0113	0.2776	-0.0264	0.0184	0.2754	-0.0589	0.1867	-16.2586	-1.661	-33.6969
14	10.3697	2.1006	0.6209	5.3389	-0.0687	0.0811	0.3271	0.638	-1.0265	-0.0515	-0.2064	0.2443	0.0706	-0.0422	-0.1207	0.3014	-0.019	-0.0873	0.3536	-0.0165	0.1744	-11.5899	5.9773	-43.5113
15	11.0838	-3.1291	12.7237	27.7132	-17.1656	21.4751	0.9517	0.1764	-0.1872	-0.6117	-0.5656	0.3636	1.2568	0.4372	-0.3861	0.4189	-0.0227	0.0129	0.8331	-0.2272	0.6323	-30.7584	2.0609	-38.1783
16	11.2865	2.1993	-5.3905	4.3716	-0.3952	11.5015	-0.5298	-0.0374	-0.8987	-0.2065	0.1904	0.1205	1.2387	-0.607	0.3394	0.2175	-0.0475	-0.0724	0.2485	-0.0778	0.3111	-24.9374	-8.4724	-2.8921
17	17.6366	-1.4292	-17.7414	0.5227	0.3236	20.932	-0.2308	0.8561	-0.5771	-0.1433	-0.0672	0.1881	0.6178	-0.7802	0.2979	0.4038	0.0295	-0.2351	0.3253	0.036	0.5169	-25.3287	1.589	-13.4521
18	11.1118	1.3707	-2.4489	13.1656	-2.0236	7.5024	0.371	-0.5743	0.1599	-0.1703	-0.4591	0.2009	0.3234	0.7075	0.0881	0.0647	0.074	-0.0351	0.2277	-0.0923	0.0842	-22.0454	-2.8343	-2.9072
19	1.5029	-0.7664	-0.6194	2.4377	-0.9915	4.7979	0.1015	0.2371	-0.4848	-0.2215	0.1869	0.0835	0.6986	-0.3835	-0.2884	0.1478	-0.0686	-0.0872	0.2322	-0.0686	0.4787	-39.5947	2.0403	-5.9538
20	42.6438	-4.6792	-15.3067	5.4136	-3.3378	10.6727	-0.8013	0.938	-2.124	0.1461	0.1124	0.4153	0.3322	-0.644	0.689	0.4116	-0.3876	0.142	0.4017	-0.114	0.586	-49.7412	2.5371	9.1079
21	5.6763	0.3546	-0.9143	7.218	0.3843	17.747	-0.0192	0.4117	-1.1536	-0.1204	0.1935	-0.5281	0.7143	0.1036	-0.1743	0.3632	-0.0485	0.0888	0.1229	-0.0302	0.3769	17.1534	-8.3511	-20.9372
22	10.8439	2.1855	-0.3826	8.9171	1.6103	9.2726	-0.1942	-0.3195	0.2841	-0.4534	-0.059	-0.1047	0.298	-0.4021	0.2532	0.0592	0.0099	0.05	0.1318	0.1079	0.1878	16.2494	-1.1933	-17.3941
23	3.2085	-5.4858	2.4223	17.8774	-2.8606	5.5432	-0.1385	0.2535	-0.3796	-0.4863	0.2153	-0.3211	0.7029	0.3564	-0.0768	0.3671	-0.1219	0.1097	0.2904	0.0471	0.3175	20.454	-1.7921	-30.099
24	8.5133	0.7964	5.1567	6.2486	0.3627	3.4111	0.3123	0.2888	-0.2658	-1.2761	0.0109	-0.5071	0.6006	0.2261	-0.3232	0.8457	0.1169	-0.02	0.2483	0.0138	0.1892	29.7625	4.608	-31.2383
25	29.4411	2.0736	-9.2691	5.7336	0.9393	10.6663	0.3373	4.4544	-0.607	-0.7697	0.8446	-0.1255	0.8681	-0.0269	-1.1818	1.0246	0.1168	-0.145	0.9637	-0.2886	0.3363	20.739	5.5195	-42.2792
26	12.7706	-0.543	-2.9057	3.2043	-1.5735	8.7688	-0.2703	-0.2772	1.4983	-0.1214	0.1698	-0.2109	-0.9724	0.1978	0.1005	0.3274	0.0244	0.0202	0.1283	-0.0117	0.3627	21.2371	36.5008	-15.7054
27	15.0743	-3.6293	7.3012	9.957	10.9616	21.3609	-0.0456	0.4881	1.2587	-0.1663	0.0285	-0.7451	-0.1959	0.4429	0.0171	0.4153	0.0574	0.1678	0.245	0.0288	0.1948	14.8505	25.4941	-24.6201
28	6.3057	-4.6401	-0.0861	4.7155	1.7429	3.2302	-0.0484	-0.2446	0.3975	0.0252	0.4054	-0.5578	-0.2388	0.0348	-0.357	0.2673	0.0901	0.0228	0.2968	-0.0689	0.2388	21.9371	27.2312	-15.6965
29	3.1136	-0.2718	0.2236	3.4196	1.0041	3.6489	-0.281	0.5102	0.821	-0.1427	0.3831	-1.0023	-0.6163	0.5328	-0.1022	0.2952	-0.0237	0.0621	0.3033	0.0508	0.7553	32.9365	30.0546	-24.9156
30	8.9342	-0.2316	6.9999	2.2234	-0.3019	11.44	-0.6415	0.3017	1.0662	-0.0641	0.1841	-0.7355	-0.1853	0.5905	0.4574	0.2143	0.0446	0.0833	0.2125	0.0749	0.5789	31.7675	20.87	-31.134

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 22
2	X-RAY DIFFRACTION	2	A	23 - 36
3	X-RAY DIFFRACTION	3	A	37 - 81
4	X-RAY DIFFRACTION	4	A	82 - 167
5	X-RAY DIFFRACTION	5	A	168 - 173
6	X-RAY DIFFRACTION	6	B	2 - 21
7	X-RAY DIFFRACTION	7	B	22 - 28
8	X-RAY DIFFRACTION	8	B	29 - 67
9	X-RAY DIFFRACTION	9	B	68 - 167
10	X-RAY DIFFRACTION	10	B	168 - 172
11	X-RAY DIFFRACTION	11	C	1 - 6
12	X-RAY DIFFRACTION	12	C	7 - 59
13	X-RAY DIFFRACTION	13	C	60 - 131
14	X-RAY DIFFRACTION	14	C	132 - 167
15	X-RAY DIFFRACTION	15	C	168 - 171
16	X-RAY DIFFRACTION	16	D	4 - 22
17	X-RAY DIFFRACTION	17	D	23 - 36
18	X-RAY DIFFRACTION	18	D	37 - 67
19	X-RAY DIFFRACTION	19	D	68 - 167
20	X-RAY DIFFRACTION	20	D	168 - 173
21	X-RAY DIFFRACTION	21	E	2 - 25
22	X-RAY DIFFRACTION	22	E	26 - 68
23	X-RAY DIFFRACTION	23	E	69 - 108
24	X-RAY DIFFRACTION	24	E	109 - 160
25	X-RAY DIFFRACTION	25	E	161 - 170
26	X-RAY DIFFRACTION	26	F	2 - 22
27	X-RAY DIFFRACTION	27	F	23 - 36
28	X-RAY DIFFRACTION	28	F	37 - 87
29	X-RAY DIFFRACTION	29	F	88 - 139
30	X-RAY DIFFRACTION	30	F	140 - 171

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