PDB-9sup: S-Adenosylmethionine synthetase of Thermococcus kodakarensis in c...

ID or keywords:

Entry

Database: PDB / ID: 9sup

Title

S-Adenosylmethionine synthetase of Thermococcus kodakarensis in complex with (S,S)-SAM and PPNP

Components

S-adenosylmethionine synthase

Keywords

TRANSFERASE / SAM Biosynthesis / Stereoselectivity / (S / S)-SAM / PPNP

Function / homology

Function and homology information

methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
Similarity search - Function

Biological species

Thermococcus kodakarensis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.66 Å

Authors

Bolz, M. / Gericke, L. / Lukat, P. / Blankenfeldt, W. / Andexer, J.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Selectivity of Methionine Adenosyltransferases regarding Methionine Enantiomers
Authors: Gericke, L. / Bolz, M. / Haeussler, M. / Kind, K. / Nagel, A. / Brenneisen, J. / Pleiss, J. / Blankenfeldt, W.

History

Deposition	Sep 29, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 7, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9sup.cif.gz	899.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9sup.ent.gz	758.5 KB	Display	PDB format
PDBx/mmJSON format	9sup.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/su/9sup ftp://data.pdbj.org/pub/pdb/validation_reports/su/9sup	HTTPS FTP

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Related structure data

Related structure data	9sq1C 9sv9C C: citing same article (ref.)
Similar structure data	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	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: S-adenosylmethionine synthase

B: S-adenosylmethionine synthase

C: S-adenosylmethionine synthase

D: S-adenosylmethionine synthase

hetero molecules

189 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	134.914, 58.868, 236.883
Angle α, β, γ (deg.)	90.00, 104.30, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 4 molecules ABCD

#1: Protein	S-adenosylmethionine synthase / AdoMet synthase / Methionine adenosyltransferase Mass: 46844.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: mat, TK0545 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: Q5JF22, methionine adenosyltransferase

#1: Protein

S-adenosylmethionine synthase / AdoMet synthase / Methionine adenosyltransferase

Mass: 46844.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermococcus kodakarensis (archaea) / Gene: mat, TK0545 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: Q5JF22, methionine adenosyltransferase

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Non-polymers , 6 types, 174 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID Mass: 256.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H₆NO₉P₃
#5: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% EG, 10% PEG 8k, 0.04 M Li Acetate, 0.1 M Tris Base pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03323 Å / Relative weight: 1
Reflection	Resolution: 2.66→67.34 Å / Num. obs: 51663 / % possible obs: 98.9 % / Redundancy: 4.4 % / CC_1/2: 0.986 / R_merge(I) obs: 0.172 / R_pim(I) all: 0.091 / R_rim(I) all: 0.195 / Χ²: 0.9 / Net I/σ(I): 7
Reflection shell	Resolution: 2.66→2.755 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.682 / Num. unique obs: 6029 / CC_1/2: 0.748 / R_pim(I) all: 0.371 / R_rim(I) all: 0.78 / Χ²: 0.78

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.66→64 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2365	2475	4.79 %
R_work	0.1853	-	-
obs	0.1877	51663	98.51 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.66→64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12463	0	87	149	12699

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	12740
X-RAY DIFFRACTION	f_angle_d	0.546	17282
X-RAY DIFFRACTION	f_dihedral_angle_d	4.414	1785
X-RAY DIFFRACTION	f_chiral_restr	0.047	1979
X-RAY DIFFRACTION	f_plane_restr	0.004	2250

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.66-2.71	0.3376	129	0.247	2725	X-RAY DIFFRACTION	99
2.71-2.77	0.3169	134	0.2369	2661	X-RAY DIFFRACTION	99
2.77-2.83	0.3058	131	0.2305	2691	X-RAY DIFFRACTION	96
2.83-2.89	0.3125	134	0.2218	2497	X-RAY DIFFRACTION	93
2.89-2.96	0.2758	154	0.2157	2750	X-RAY DIFFRACTION	99
2.96-3.04	0.2651	141	0.2146	2712	X-RAY DIFFRACTION	99
3.04-3.13	0.2941	136	0.2116	2730	X-RAY DIFFRACTION	100
3.13-3.24	0.2534	135	0.2141	2762	X-RAY DIFFRACTION	100
3.24-3.35	0.2557	143	0.194	2776	X-RAY DIFFRACTION	100
3.35-3.48	0.2396	129	0.1866	2765	X-RAY DIFFRACTION	100
3.48-3.64	0.2414	142	0.1816	2744	X-RAY DIFFRACTION	100
3.64-3.84	0.2103	146	0.1669	2755	X-RAY DIFFRACTION	100
3.84-4.08	0.1861	153	0.1552	2760	X-RAY DIFFRACTION	100
4.08-4.39	0.2014	143	0.1533	2736	X-RAY DIFFRACTION	100
4.39-4.83	0.211	117	0.151	2810	X-RAY DIFFRACTION	99
4.83-5.53	0.2348	141	0.168	2614	X-RAY DIFFRACTION	94
5.53-6.97	0.218	119	0.1965	2784	X-RAY DIFFRACTION	98
6.97-64	0.1971	148	0.1792	2916	X-RAY DIFFRACTION	100

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	3.0884	1.1034	0.0981	2.3645	1.4524	3.4617	0.0186	-0.4014	-0.0296	0.3245	-0.1558	0.1207	-0.0086	-0.0963	0.1264	0.3279	-0.0151	0.0111	0.0894	0.0863	0.2586	17.1159	2.392	100.8941
2	6.9774	0.6303	1.6128	0.7435	0.3294	1.9606	0.1858	0.2968	-0.0705	0.0427	-0.1039	-0.0108	0.0569	0.1093	-0.0847	0.2413	0.0283	0.046	0.1433	-0.0158	0.1937	25.7233	-5.6694	69.869
3	2.3945	-0.4733	-3.3514	0.396	0.3482	5.1047	0.0149	-0.363	-0.1054	0.0799	0.0473	-0.4006	-0.1252	0.7868	-0.0632	0.3381	0.002	-0.0703	0.3771	-0.037	0.381	36.7306	2.3827	90.5519
4	1.5077	0.7271	0.7451	1.2236	0.4841	1.9111	0.0478	-0.0909	-0.1643	0.0502	-0.0737	0.115	0.2337	-0.2732	0.0239	0.2691	-0.0184	0.023	0.255	-0.0195	0.3209	4.7896	-8.1456	83.6841
5	2.5017	-0.4647	-0.7705	0.6981	0.8308	4.3124	0.0595	-0.1733	-0.1568	0.1537	-0.0113	0.0213	0.3726	0.2162	-0.0277	0.3022	-0.0044	-0.0005	0.1706	0.0227	0.2327	27.0057	-1.6781	101.0936
6	0.7964	0.443	-0.04	0.2926	0.5267	2.6164	0.1128	-0.0557	0.0736	-0.0832	-0.0832	-0.017	-0.1841	-0.1781	-0.0435	0.3395	0.064	0.0314	0.1194	0.0087	0.2666	32.9849	11.1959	35.1433
7	0.8321	0.1962	-0.4007	0.716	0.8121	3.8794	0.008	-0.1243	0.2016	-0.0822	-0.0527	-0.1321	-0.3647	0.1519	0.0446	0.264	-0.0481	0.0098	0.1897	0.0033	0.2883	36.2098	12.5347	47.8408
8	2.9377	-1.5476	-1.2662	1.5872	1.2726	1.8163	-0.0738	-0.0078	0.1182	-0.3254	-0.2075	0.2533	-1.2515	-1.0186	0.1677	0.6467	0.3091	-0.1105	0.6214	-0.0784	0.4052	13.9271	19.0636	25.7978
9	1.3624	0.0563	-1.1322	0.6939	0.0929	4.4793	0.0518	0.0477	0.1695	-0.0972	-0.0129	-0.0796	-0.3233	0.2323	-0.0411	0.287	-0.0278	0.0052	0.2213	0.0267	0.2399	42.1014	9.8005	25.8975
10	1.8671	0.6702	-0.0429	1.4886	0.1946	1.2279	-0.0003	-0.2416	0.242	0.1609	-0.0859	0.0512	-0.0468	0.0002	0.0893	0.2753	-0.04	0.0234	0.2926	-0.0417	0.2882	11.2774	15.6563	96.2137
11	3.635	1.1789	1.3053	0.7038	0.424	0.611	0.1305	0.1295	0.2257	-0.0136	-0.0868	0.093	-0.0195	0.0225	-0.017	0.2788	0.0529	0.0249	0.2144	-0.02	0.2165	14.7587	16.8688	68.008
12	8.6231	0.7983	1.0358	1.4274	0.0468	1.2785	0.1348	0.3725	0.1803	-0.056	-0.1338	0.1186	-0.1447	0.0841	0.0034	0.3047	0.0162	0.0147	0.1707	-0.0048	0.1487	16.3724	15.9592	61.4868
13	3.2665	0.3707	5.6253	1.2754	1.1198	9.7884	0.5431	0.2345	-0.0493	-0.0942	-0.1474	0.3198	0.5398	-0.2051	-0.4427	0.2477	0.0544	0.0354	0.4365	-0.0418	0.3637	-3.5086	12.014	77.9745
14	3.0095	0.9402	-1.5803	1.5269	-1.0423	4.5145	0.0621	-0.2264	0.2662	0.0443	-0.0652	-0.1024	-0.5479	0.4265	0.0178	0.3266	-0.0932	-0.0048	0.2334	-0.07	0.3278	31.5498	27.7255	86.8085
15	2.8448	0.0894	-1.1011	0.3471	-0.0945	1.5048	-0.0085	0.046	0.1068	0.0364	0.0548	-0.0253	-0.0219	-0.0791	-0.0451	0.2733	0.0096	-0.0245	0.1764	-0.0101	0.2859	10.4361	15.2472	85.0672
16	1.115	0.4277	-0.0371	1.8307	-0.3136	3.7743	0.0147	-0.0739	0.1949	0.2516	0.0227	0.2011	-0.1452	-0.4083	-0.0244	0.2408	0.0766	0.0238	0.2623	-0.0661	0.2935	-0.4795	20.4325	91.7723
17	0.8224	0.0672	-0.0982	0.1803	-0.3234	1.7456	0.0361	0.0325	0.0283	-0.1132	-0.0256	-0.0184	0.0943	-0.013	-0.0144	0.2625	0.0111	0.009	0.1347	-0.0293	0.2254	24.627	-7.3854	35.6794
18	3.7148	-0.933	3.7887	2.9244	-1.6449	4.3914	-0.1598	-0.5813	0.7488	-0.0154	0.0733	0.2873	-0.101	-0.5881	0.0703	0.2531	0.0182	0.0577	0.2361	-0.1101	0.2132	15.4422	-2.6143	52.6086
19	7.7222	-1.6809	1.2821	0.8563	-0.6093	1.414	0.0807	-0.6195	-0.457	-0.0052	-0.1428	0.1119	0.1009	-0.0009	0.0957	0.2894	-0.031	0.0069	0.2518	0.0354	0.2836	23.5574	-13.0448	53.2991
20	0.501	0.1788	-0.1728	0.4965	-0.3694	2.9756	0.057	-0.0075	0.2007	0.0103	0.0142	0.319	-0.0106	-0.3743	-0.0821	0.3222	0.0101	0.0062	0.2233	-0.0319	0.4069	12.8594	-0.9678	35.1508
21	1.9089	-0.2619	1.0362	1.319	-1.0888	5.392	0.0829	0.0088	-0.1819	-0.086	-0.0282	-0.1093	0.2543	0.2718	-0.0523	0.2366	0.0734	0.0199	0.1792	-0.0236	0.2948	44.3217	-18.1037	38.8305
22	1.0609	-0.2415	0.2643	1.5793	0.4731	2.2414	0.0402	0.1111	-0.1452	-0.1311	-0.0246	0.0303	0.1101	-0.1461	-0.0117	0.2085	-0.0011	0.0082	0.1951	-0.0071	0.1978	21.2327	-8.0898	23.353

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 33 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 144 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 145 through 173 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 174 through 316 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 317 through 405 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 82 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 83 through 173 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 174 through 277 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 278 through 405 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 4 through 33 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 34 through 82 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 83 through 144 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 145 through 173 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 174 through 269 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 270 through 358 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 359 through 405 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 3 through 82 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 83 through 106 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 107 through 131 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 132 through 173 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 174 through 277 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 278 through 405 )

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Experimental details

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