PDB-2p5x: Crystal structure of Maf domain of human N-acetylserotonin O-meth...

ID or keywords:

Entry

Database: PDB / ID: 2p5x

Title

Crystal structure of Maf domain of human N-acetylserotonin O-methyltransferase-like protein

Components

N-acetylserotonin O-methyltransferase-like protein

Keywords

CELL CYCLE /

asmtl /

Structural Genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

dTTP diphosphatase activity / UTP diphosphatase activity /

nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process /

O-methyltransferase activity /

Transferases; Transferring one-carbon groups; Methyltransferases /

methylation /

cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

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

Citation

Journal: Chem.Biol. / Year: 2013
Title: Biochemical and structural studies of conserved maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides.
Authors: Tchigvintsev, A. / Tchigvintsev, D. / Flick, R. / Popovic, A. / Dong, A. / Xu, X. / Brown, G. / Lu, W. / Wu, H. / Cui, H. / Dombrowski, L. / Joo, J.C. / Beloglazova, N. / Min, J. / ...

History

Deposition	Mar 16, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2007	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	Nov 20, 2013	Group: Database references / Structure summary
Revision 1.4	Jan 15, 2014	Group: Database references
Revision 1.5	Aug 30, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	2p5x.cif.gz	103.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p5/2p5x ftp://data.pdbj.org/pub/pdb/validation_reports/p5/2p5x	HTTPS FTP

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Related structure data

Related structure data	4hebC 4jhcC 4lu1C 1ex2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ib2-1 4uhp-1 4een-d 3szm-7 3mpk-d 3vqm-3 3al3-d 6o31-d 6ydm-1 4m0h-2 Search similar-shape structures by Omokage search (details) 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: N-acetylserotonin O-methyltransferase-like protein

B: N-acetylserotonin O-methyltransferase-like protein

hetero molecules

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

1

A: N-acetylserotonin O-methyltransferase-like protein

hetero molecules

defined by author
25.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N-acetylserotonin O-methyltransferase-like protein

hetero molecules

defined by author
25.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.802, 116.983, 51.471
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	N-acetylserotonin O-methyltransferase-like protein / / ASMTL Mass: 25819.490 Da / Num. of mol.: 2 / Fragment: MAF domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASMTL / Plasmid: pET28a-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95671
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.47 Å³/Da / Density % sol: 50.22 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 3350, 0.1 M Succinic acid, 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: 1.54 Å
Detector	Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jan 28, 2007
Radiation	Monochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2→25.07 Å / Num. all: 35334 / Num. obs: 35334 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / R_merge(I) obs: 0.167 / Net I/σ(I): 5.9

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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
Starting model: PDB entry 1EX2

1ex2

Resolution: 2→25.07 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.918 / SU B: 8.768 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25309	1764	5 %	RANDOM
R_work	0.19795	-	-	-
all	0.20077	33495	-	-
obs	0.20077	33495	99.82 %	-

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: 23.982 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	-0.06 Å²

Refinement step

Cycle: LAST / Resolution: 2→25.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3190	0	10	333	3533

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3262
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.429	1.972	4401
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.31	5	402
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.186	23.681	144
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.282	15	581
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.525	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	489
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2424
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1453
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.298	0.2	2189
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	283
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	0.166	0.2	41
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.18	0.2	27
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	0.804	1.5	2066
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.356	2	3222
X-RAY DIFFRACTION	r_scbond_it	1.905	3	1349
X-RAY DIFFRACTION	r_scangle_it	3.016	4.5	1179
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.053 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	123	-
R_work	0.279	2411	-
obs	-	-	98.75 %

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	3.5153	-2.1261	0.6714	1.2939	-0.3619	0.4166	-0.0314	-0.2753	-0.4159	-0.0956	0.0701	0.27	-0.0249	-0.0992	-0.0386	0.0088	-0.027	0.0161	0.0615	0.0481	0.0843	39.4581	29.2015	51.8753
2	7.5272	-0.3502	-6.2128	0.5997	-2.3878	17.4104	0.1078	-0.1337	-0.4315	-0.0839	0.0105	0.2804	-0.3028	-0.3114	-0.1183	0.0202	-0.0206	-0.0014	0.0051	-0.0009	0.0892	43.1403	22.0058	52.4447
3	3.8575	2.8569	-2.5923	3.8817	-2.7655	9.8208	-0.102	0.1685	0.0491	-0.1489	0.2603	0.1897	-0.0458	0.092	-0.1583	-0.0213	-0.0178	-0.0032	0.0544	-0.0017	0.033	40.6322	32.329	43.0349
4	5.3325	1.6689	3.4061	5.8692	-0.4099	5.7535	0.0565	0.0827	0.3081	-0.4467	0.0938	0.1152	0.1563	0.1882	-0.1503	0.0721	-0.0058	-0.0158	-0.0018	0.0336	0.0448	59.4425	38.9965	37.9264
5	5.9775	-1.1248	-0.2449	0.2385	0.0446	0.0101	0.1393	0.0868	0.0722	-0.0511	-0.0886	-0.046	-0.0025	-0.0358	-0.0507	0.0433	-0.004	0.0023	0.0302	0.0203	0.0846	46.6138	38.8395	44.1375
6	0.1695	-0.3117	0.1355	0.8709	-0.2289	0.1097	0.0507	0.0237	0.0491	-0.0465	-0.0189	-0.0117	0.0203	-0.0787	-0.0317	0.0453	0.0054	-0.0002	0.0593	0.0032	0.0603	48.8824	33.073	45.184
7	2.2588	-0.613	0.8707	7.7789	-0.1686	4.2408	-0.0638	0.1367	0.2083	-0.9042	0.0592	0.0651	0.1687	-0.1532	0.0046	0.1675	-0.0397	-0.003	0.0454	0.0016	-0.0394	58.1251	20.466	30.5001
8	2.9622	-2.4199	-0.8213	2.4323	0.7341	0.3242	-0.11	-0.0312	0.1511	0.0691	0.0548	-0.1447	0.0846	-0.0483	0.0552	0.0559	-0.0011	-0.0028	0.0411	0.0002	0.0412	55.4668	30.3791	46.8944
9	8.8201	-5.691	1.1076	4.0492	-0.6615	0.2528	-0.1555	-0.2433	0.5318	0.1573	0.1005	-0.3875	-0.0653	-0.031	0.055	0.0548	0.0149	0.0082	0.0369	-0.0198	0.0525	47.0565	41.5805	52.0842
10	1.1102	0.909	0.7443	0.7469	0.4979	5.2722	-0.0963	-0.0004	0.0075	-0.2977	0.1243	-0.2265	0.2599	0.2524	-0.028	0.1636	0.0114	0.0276	0.0125	-0.0047	0.0525	65.4728	12.8201	38.8558
11	11.2867	-0.0942	-2.8397	5.5064	6.3852	8.1911	-0.5956	0.4882	-0.215	0.0015	0.3793	0.1764	1.0684	-0.3199	0.2164	0.2022	-0.1174	0.0278	0.0392	-0.0369	-0.0727	55.4731	11.1016	32.3249
12	1.3317	-1.4372	1.7074	6.5095	-2.9448	2.434	0.0881	-0.1576	0.0081	-0.1825	-0.1546	0.2979	0.4304	-0.3177	0.0664	0.0738	-0.0558	0.0165	0.0719	-0.0252	0.0327	55.7297	14.587	40.6579
13	0.559	-0.7139	0.4102	7.15	-1.2601	0.3878	-0.2079	-0.0126	0.0661	-0.1117	0.2127	0.0107	-0.1043	0.0884	-0.0049	0.0539	0.0037	0.0087	0.0453	0.0072	0.0395	61.9811	16.2411	50.885
14	1.7902	-1.8222	0.5125	4.7705	2.4482	3.1717	-0.0879	-0.1248	-0.2581	0.1077	0.0405	0.0959	-0.0045	-0.0283	0.0474	0.0183	-0.019	0.0136	0.0597	0.0047	0.0501	51.5659	27.0205	56.1288
15	23.2024	5.3772	18.3309	2.1954	-0.4159	37.3996	0.0299	-1.9234	-1.1367	0.2537	0.3549	-0.0476	-1.0033	-0.2026	-0.3848	0.0699	0.1277	0.0535	0.0067	-0.0362	0.0355	47.2271	36.8462	64.8237
16	0.6387	-0.4229	-0.8462	5.307	1.5081	1.2998	-0.0338	0.0461	-0.1014	-0.4316	-0.1282	0.3036	-0.0893	-0.1603	0.1621	0.0678	0.0061	-0.0441	0.0341	0.0065	0.0487	54.6196	-8.4313	44.4968
17	2.8573	2.65	-6.6185	5.8827	-3.2605	17.7481	0.0449	0.0681	0.4476	-0.0215	0.1239	0.5426	-0.1249	-0.2138	-0.1688	0.0179	-0.0003	-0.0302	0.015	-0.0009	0.1101	51.5447	0.9127	49.3682
18	2.2063	-0.4623	3.1476	9.8848	-5.5861	6.9721	-0.1214	0.0352	-0.0138	-0.6498	0.023	0.3661	0.0149	0.0708	0.0984	0.0468	0.001	-0.0484	0.0155	-0.0112	0.0461	51.6782	-6.168	45.1877
19	13.2666	14.5172	8.0136	16.1431	7.4482	11.6192	0.4967	-0.873	-0.1711	1.1448	-0.9005	0.013	0.1444	-0.9196	0.4038	0.0955	0.0245	-0.018	0.0388	-0.0351	0.008	62.6463	-10.4321	66.1416
20	1.2081	1.3903	1.0441	2.88	0.7985	1.0292	0.0155	-0.0618	-0.062	0.1421	-0.0425	-0.1319	0.0003	-0.1442	0.0271	0.0448	0.0072	-0.0135	0.0297	-0.0009	0.0666	62.4687	-11.258	56.8603
21	0.5865	-0.6354	-1.0094	5.2481	2.7144	2.3132	0.0942	0.0292	-0.0702	-0.2015	-0.044	-0.0774	-0.1011	-0.1341	-0.0502	0.03	-0.0101	-0.0428	0.0391	0.0026	0.0443	56.5677	-15.6315	48.0033
22	3.0117	0.6258	-0.3841	5.9176	3.5435	3.0653	0.1263	-0.3582	-0.0162	0.5518	-0.4028	0.0136	0.4147	-0.1957	0.2765	0.1366	-0.0618	0.0212	0.0729	-0.0078	-0.0681	55.5385	5.7385	70.829
23	0.7036	-2.6037	-1.6505	10.4564	6.6954	4.2922	-0.05	-0.0682	-0.0348	-0.1348	0.0275	-0.0098	-0.0203	0.1559	0.0225	0.0543	-0.0087	-0.0035	0.0436	0.0177	0.0512	63.463	4.9968	59.6725
24	5.8734	-0.6965	1.1002	8.3184	1.1649	2.3383	0.0815	0.5426	-0.3157	-0.6929	0.1717	-0.2299	-0.0272	0.1688	-0.2532	0.0771	-0.0134	0.0283	0.0854	-0.0489	0.0149	63.8028	-22.0884	42.839
25	0.8876	0.1781	-0.1905	2.3401	-0.0511	0.041	0.0882	-0.0046	0.1114	-0.2734	0.0397	-0.4839	-0.0938	0.0235	-0.1279	0.0456	0.014	-0.0308	0.0393	0.0079	0.0051	64.6524	1.4323	55.4813
26	8.0474	0.6102	7.5086	27.1261	12.5104	15.8754	0.6419	-0.4486	-0.0244	0.4583	-1.7481	1.8262	-1.7486	-2.1378	1.1062	-0.1653	0.0457	0.1341	0.3727	-0.3049	-0.0604	45.7567	14.9607	70.5932
27	16.7402	-10.8798	5.3839	19.3133	12.6235	22.9644	-0.7475	-0.124	-0.4993	-0.1123	-1.1825	0.9814	1.3012	-3.3471	1.93	-0.185	-0.1799	0.0692	0.46	-0.3133	0.1109	44.7842	5.592	65.2237
28	14.7772	5.7792	1.2907	9.3856	-1.5274	0.6923	-0.0285	0.3259	0.5227	-0.6251	0.2627	0.5118	0.1908	0.1584	-0.2342	0.0704	-0.0452	-0.0136	0.0774	-0.0111	0.0012	51.9031	8.1474	61.0456
29	0.0836	-0.3475	-0.1729	1.4667	0.515	2.2788	0.0058	0.0733	-0.0924	-0.0198	0.03	-0.0188	-0.0646	-0.226	-0.0359	0.0391	-0.0063	-0.0002	0.0612	-0.0053	0.0556	59.2663	9.7373	53.5147
30	11.2382	-0.7212	-9.1928	7.0291	1.2192	7.5763	-0.7204	0.442	-0.525	-0.7376	0.0865	-0.2724	0.1621	-0.3157	0.6338	0.1688	-0.0134	0.1113	0.0248	-0.0699	0.0154	68.3356	-2.9199	40.0837

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	10 - 23	1 - 14
2	X-RAY DIFFRACTION	2	A	A	24 - 33	15 - 24
3	X-RAY DIFFRACTION	3	A	A	34 - 44	25 - 35
4	X-RAY DIFFRACTION	4	A	A	45 - 52	36 - 43
5	X-RAY DIFFRACTION	5	A	A	53 - 76	44 - 67
6	X-RAY DIFFRACTION	6	A	A	77 - 98	68 - 89
7	X-RAY DIFFRACTION	7	A	A	99 - 112	90 - 103
8	X-RAY DIFFRACTION	8	A	A	113 - 133	104 - 124
9	X-RAY DIFFRACTION	9	A	A	134 - 147	125 - 138
10	X-RAY DIFFRACTION	10	A	A	148 - 160	139 - 151
11	X-RAY DIFFRACTION	11	A	A	161 - 169	152 - 160
12	X-RAY DIFFRACTION	12	A	A	170 - 185	161 - 176
13	X-RAY DIFFRACTION	13	A	A	186 - 193	177 - 184
14	X-RAY DIFFRACTION	14	A	A	194 - 209	185 - 200
15	X-RAY DIFFRACTION	15	A	A	210 - 213	201 - 204
16	X-RAY DIFFRACTION	16	B	B	10 - 22	1 - 13
17	X-RAY DIFFRACTION	17	B	B	23 - 29	14 - 20
18	X-RAY DIFFRACTION	18	B	B	30 - 40	21 - 31
19	X-RAY DIFFRACTION	19	B	B	41 - 51	32 - 42
20	X-RAY DIFFRACTION	20	B	B	52 - 74	43 - 65
21	X-RAY DIFFRACTION	21	B	B	75 - 89	66 - 80
22	X-RAY DIFFRACTION	22	B	B	90 - 116	81 - 107
23	X-RAY DIFFRACTION	23	B	B	117 - 127	108 - 118
24	X-RAY DIFFRACTION	24	B	B	128 - 136	119 - 127
25	X-RAY DIFFRACTION	25	B	B	137 - 154	128 - 145
26	X-RAY DIFFRACTION	26	B	B	155 - 164	146 - 155
27	X-RAY DIFFRACTION	27	B	B	165 - 171	156 - 162
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