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- PDB-9sv9: S-Adenosylmethionine synthetase of Escherichia coli I103A in comp... -

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Open data

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Basic information

Entry

Database: PDB / ID: 9sv9

Title

S-Adenosylmethionine synthetase of Escherichia coli I103A in complex with (S,S)-SAM and PPNP

Components

S-adenosylmethionine synthase

Keywords

TRANSFERASE / SAM Biosynthesis / Stereoselectivity / (S / S)-SAM / L-SAM / PPNP / L-Methionine / APPNP

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

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

Funding support

Germany, 1items

Citation

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

History

Deposition	Oct 2, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 14, 2026	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9sv9.cif.gz	433.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9sv9.ent.gz	360.7 KB	Display	PDB format
PDBx/mmJSON format	9sv9.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/sv/9sv9 ftp://data.pdbj.org/pub/pdb/validation_reports/sv/9sv9	HTTPS FTP

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Related structure data

Related structure data	9sq1C 9supC 9suw PDB Unreleased entry 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)

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Assembly

Deposited unit

B: S-adenosylmethionine synthase

D: S-adenosylmethionine synthase

hetero molecules

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

1

B: S-adenosylmethionine synthase

D: S-adenosylmethionine synthase

hetero molecules

B: S-adenosylmethionine synthase

D: S-adenosylmethionine synthase

hetero molecules

B: S-adenosylmethionine synthase

D: S-adenosylmethionine synthase

hetero molecules

B: S-adenosylmethionine synthase

D: S-adenosylmethionine synthase

hetero molecules

defined by author
Evidence: gel filtration
341 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.228, 122.228, 287.638
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

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Components

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Protein , 1 types, 2 molecules BD

#1: Protein

S-adenosylmethionine synthase / AdoMet synthase / MAT / Methionine adenosyltransferase

Mass: 41825.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: metK, EcE24377A_3284 / Production host:

Escherichia coli (E. coli) / References: UniProt: A7ZR64, methionine adenosyltransferase

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Non-polymers , 6 types, 268 molecules

#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID Mass: 256.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₆NO₉P₃
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: K
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 255 / 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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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.71 Å³/Da / Density % sol: 66.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.56 Details: 23.3% EG, 9.5% PEG 8k, 0.029 M Lithium sulfate, 0.1 M Tris Base pH 8.56

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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: 1.033176 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033176 Å / Relative weight: 1
Reflection	Resolution: 1.99→105.8 Å / Num. obs: 87996 / % possible obs: 100 % / Redundancy: 40.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.36 / R_pim(I) all: 0.057 / R_rim(I) all: 0.364 / Χ²: 0.91 / Net I/σ(I): 12.6 / Num. measured all: 3541750
Reflection shell	Resolution: 1.99→2.09 Å / % possible obs: 100 % / Redundancy: 40 % / R_merge(I) obs: 4.794 / Num. measured all: 504460 / Num. unique obs: 12623 / CC_1/2: 0.513 / R_pim(I) all: 0.765 / R_rim(I) all: 4.855 / Χ²: 0.81 / Net I/σ(I) obs: 1.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.09→99.34 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1986	3907	5.17 %
R_work	0.1764	-	-
obs	0.1775	75579	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.09→99.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5813	0	89	255	6157

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6013
X-RAY DIFFRACTION	f_angle_d	0.775	8178
X-RAY DIFFRACTION	f_dihedral_angle_d	7.121	848
X-RAY DIFFRACTION	f_chiral_restr	0.048	918
X-RAY DIFFRACTION	f_plane_restr	0.007	1063

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 (%)
2.09-2.12	0.2602	138	0.2793	2528	X-RAY DIFFRACTION	100
2.12-2.14	0.2401	170	0.2504	2479	X-RAY DIFFRACTION	100
2.14-2.17	0.2611	137	0.2423	2491	X-RAY DIFFRACTION	100
2.17-2.2	0.2318	146	0.2265	2522	X-RAY DIFFRACTION	100
2.2-2.23	0.2371	141	0.218	2506	X-RAY DIFFRACTION	100
2.23-2.27	0.2404	138	0.208	2517	X-RAY DIFFRACTION	100
2.27-2.3	0.2032	143	0.2073	2511	X-RAY DIFFRACTION	100
2.3-2.34	0.18	129	0.1927	2520	X-RAY DIFFRACTION	100
2.34-2.38	0.2103	127	0.1884	2539	X-RAY DIFFRACTION	100
2.38-2.42	0.2191	141	0.1766	2502	X-RAY DIFFRACTION	100
2.42-2.47	0.174	135	0.181	2539	X-RAY DIFFRACTION	100
2.47-2.52	0.1982	130	0.1814	2543	X-RAY DIFFRACTION	100
2.52-2.58	0.1806	135	0.1749	2520	X-RAY DIFFRACTION	100
2.58-2.64	0.1813	135	0.1679	2532	X-RAY DIFFRACTION	100
2.64-2.7	0.2163	155	0.1653	2522	X-RAY DIFFRACTION	100
2.7-2.78	0.1869	144	0.1731	2551	X-RAY DIFFRACTION	100
2.78-2.86	0.2002	137	0.1629	2537	X-RAY DIFFRACTION	100
2.86-2.95	0.2138	144	0.1703	2543	X-RAY DIFFRACTION	100
2.95-3.05	0.1928	154	0.1627	2543	X-RAY DIFFRACTION	100
3.05-3.18	0.1838	130	0.162	2543	X-RAY DIFFRACTION	100
3.18-3.32	0.2251	126	0.1624	2584	X-RAY DIFFRACTION	100
3.32-3.5	0.1929	133	0.1535	2591	X-RAY DIFFRACTION	100
3.5-3.72	0.1821	140	0.1654	2591	X-RAY DIFFRACTION	100
3.72-4	0.1735	131	0.159	2597	X-RAY DIFFRACTION	100
4-4.4	0.1799	131	0.1556	2632	X-RAY DIFFRACTION	100
4.41-5.04	0.1726	145	0.1556	2637	X-RAY DIFFRACTION	100
5.04-6.35	0.2342	150	0.2019	2669	X-RAY DIFFRACTION	100
6.35-99.34	0.2092	142	0.2	2883	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	1.4229	-0.1888	-0.1534	3.27	1.7515	3.2285	-0.0359	-0.082	0.1877	-0.1755	0.0347	-0.0675	-0.124	-0.0533	0.0204	0.3051	0.0008	-0.0576	0.2183	-0.0161	0.2379	-35.6723	74.3757	18.5456
2	5.9195	0.4322	4.1134	2.1811	-0.391	8.9502	-0.176	-0.2683	0.0982	-0.1787	0.0876	0.018	0.1738	-0.3178	0.0553	0.439	0.0207	-0.0214	0.1842	-0.023	0.2698	-37.4979	60.3011	12.4931
3	0.4127	0.3615	0.4285	1.1571	0.1629	1.0365	-0.0409	0.1333	0.0516	-0.2784	0.0158	0.0811	0.0298	0.0431	-0.0096	0.4117	0.0432	-0.0071	0.245	-0.0197	0.203	-32.7157	61.9369	14.1502
4	1.869	0.2509	0.5107	0.9676	-0.0805	1.6216	-0.0159	-0.0597	0.3663	-0.151	-0.0701	0.1829	-0.0601	-0.0589	0.0297	0.3965	0.051	-0.1745	0.2409	-0.0152	0.3609	-50.4301	81.5394	13.9012
5	2.3155	-0.0217	0.1969	1.728	0.0775	1.7811	-0.1358	-0.1844	0.3952	-0.2016	0.1249	-0.1248	-0.3084	0.1171	0.0413	0.3492	-0.0327	-0.0765	0.2723	-0.0901	0.3799	-25.8787	86.3858	26.9169
6	1.3401	0.0681	0.4123	0.8656	0.113	0.9909	-0.1189	-0.0986	0.2536	-0.1872	0.1136	0.1196	-0.11	-0.0369	0.0552	0.4146	0.0198	-0.1229	0.2742	-0.0537	0.3493	-43.6615	82.7421	20.6044
7	3.3176	-1.3333	0.6905	2.0477	-0.4866	1.78	-0.0614	-0.0412	0.4487	-0.3754	0.0227	0.1184	-0.2798	-0.2513	0.0501	0.5295	-0.0211	-0.1627	0.2607	0.0245	0.3662	-48.5797	83.8052	6.3404
8	1.3286	0.0236	-0.1261	1.6977	-0.4853	1.4388	-0.0788	-0.1039	-0.258	-0.0405	-0.0106	-0.0592	0.0029	0.0605	0.0191	0.3601	0.0127	0.0653	0.2232	0.0186	0.2542	-30.7425	28.5483	16.081
9	2.5085	0.3047	-1.0907	1.2548	-0.447	3.0815	-0.1869	-0.113	-0.0034	-0.1635	-0.0012	-0.0314	0.0257	0.0109	0.0325	0.4453	0.0076	0.0505	0.2607	-0.0192	0.2615	-29.6914	44.295	11.3809
10	2.7204	0.3578	-0.4204	2.201	-0.0244	0.9593	-0.0634	-0.0192	0.0628	-0.126	0.0363	0.2131	-0.0135	-0.1885	0.0063	0.417	0.0132	-0.0266	0.3116	0.0039	0.2892	-44.6301	39.1405	16.6427
11	0.2136	0.0433	0.2054	1.3304	0.1416	0.6386	0.0191	-0.3168	0.0698	-0.3252	0.046	-0.4978	-0.1092	0.5669	0.0065	0.5307	0.0109	0.0795	0.3344	0.0273	0.3194	-17.1127	47.3843	6.5835
12	1.809	0.2509	-0.2443	1.3102	-0.4008	1.254	-0.0335	-0.0476	-0.3455	-0.2147	-0.0457	-0.0887	0.1304	0.0101	0.0893	0.454	0.0124	0.167	0.246	-0.0086	0.3485	-16.5684	23.1041	8.6713
13	1.6575	0.4645	0.0395	1.386	-0.1668	0.9034	-0.0344	-0.1774	-0.3955	-0.1131	0.0319	0.0342	0.182	-0.103	-0.0009	0.3753	-0.0016	0.0817	0.2812	0.0801	0.3624	-36.2004	19.0939	22.5001
14	2.4314	0.0841	-0.11	2.1898	0.4305	1.6735	-0.1597	-0.1123	-0.3966	-0.3137	0.1105	-0.3036	0.2313	-0.0344	0.0708	0.4999	0.0003	0.1984	0.2908	0.0108	0.386	-15.6557	19.8043	7.368
15	1.503	-0.1978	-0.0649	1.4469	0.0481	1.0633	-0.0956	0.078	-0.3408	-0.5453	-0.0007	-0.2373	0.2622	0.0828	0.0894	0.5666	-0.0037	0.2145	0.2335	-0.0095	0.3737	-16.0774	21.3275	2.9792

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 33 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 34 through 63 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 64 through 110 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 111 through 135 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 136 through 205 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 206 through 321 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 322 through 382 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 1 through 33 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 34 through 63 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 64 through 89 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 90 through 110 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 111 through 135 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 136 through 269 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 270 through 300 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 301 through 382 )

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