PDB-7lnn: E. coli S-adenosyl methionine transferase co-crystallized with gu...

ID or keywords:

Entry

Database: PDB / ID: 7lnn

Title

E. coli S-adenosyl methionine transferase co-crystallized with guanosine-5'-imidotriphosphate

Components

S-adenosylmethionine synthase

Keywords

TRANSFERASE / S-adenosyl methionine transferase

Function / homology

Function and homology information

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

Biological species

Escherichia coli 908573 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Tan, L.L. / Jackson, C.J.

Citation

Journal: Jacs Au / Year: 2021
Title: Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases.
Authors: Gade, M. / Tan, L.L. / Damry, A.M. / Sandhu, M. / Brock, J.S. / Delaney, A. / Villar-Briones, A. / Jackson, C.J. / Laurino, P.

History

Deposition	Feb 8, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 31, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7lnn.cif.gz	371.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7lnn.ent.gz	257.2 KB	Display	PDB format
PDBx/mmJSON format	7lnn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7lnn_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7lnn_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7lnn_validation.xml.gz	29.4 KB	Display
Data in CIF	7lnn_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ln/7lnn ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lnn	HTTPS FTP

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Related structure data

Related structure data	7ll3C 7lnhC 7lo2C 7looC 7lowC 7lozC 1p7lS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7low-1 7ll3-1 7lo2-d 1mxb-2 7loz-1 1mxc-2 6rkc-1 1xra-2 1fug-1 3rv2-2 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: S-adenosylmethionine synthase

B: S-adenosylmethionine synthase

hetero molecules

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

1

A: S-adenosylmethionine synthase

B: S-adenosylmethionine synthase

hetero molecules

A: S-adenosylmethionine synthase

B: S-adenosylmethionine synthase

hetero molecules

defined by author&software
Evidence: gel filtration
170 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.336, 122.336, 287.267
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

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Protein , 1 types, 2 molecules AB

#1: Protein	S-adenosylmethionine synthase / AdoMet synthase / MAT / Methionine adenosyltransferase Mass: 41998.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli 908573 (bacteria) / Gene: metK, HMPREF1611_00479 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZE41, methionine adenosyltransferase

#1: Protein

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

Mass: 41998.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli 908573 (bacteria) / Gene: metK, HMPREF1611_00479 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZE41, methionine adenosyltransferase

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Non-polymers , 5 types, 89 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID Mass: 256.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₆NO₉P₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 3.69 Å³/Da / Density % sol: 66.7 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop Details: 8% OEG 8000, 0.1 M Bis-Tris pH 6.5, 20% ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.5→43.63 Å / Num. obs: 44910 / % possible obs: 100 % / Redundancy: 39.1 % / B_iso Wilson estimate: 71 Å² / CC_1/2: 0.999 / Net I/σ(I): 16.2
Reflection shell	Resolution: 2.5→2.59 Å / Num. unique obs: 4600 / CC_1/2: 0.675

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1P7L

1p7l

Resolution: 2.5→43.63 Å / SU ML: 0.3811 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2426	2229	5 %
R_work	0.2222	42344	-
obs	0.2233	44573	99.45 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 95.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→43.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5790	0	49	80	5919

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0023	6063
X-RAY DIFFRACTION	f_angle_d	0.5732	8239
X-RAY DIFFRACTION	f_chiral_restr	0.0445	916
X-RAY DIFFRACTION	f_plane_restr	0.0039	1075
X-RAY DIFFRACTION	f_dihedral_angle_d	19.4674	2248

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 (%)
2.5-2.55	0.399	125	0.3587	2594	X-RAY DIFFRACTION	99.41
2.55-2.61	0.4061	141	0.3251	2581	X-RAY DIFFRACTION	99.6
2.61-2.68	0.3387	133	0.3142	2595	X-RAY DIFFRACTION	99.6
2.68-2.75	0.3783	123	0.3116	2606	X-RAY DIFFRACTION	99.71
2.75-2.83	0.3776	125	0.3058	2632	X-RAY DIFFRACTION	99.78
2.83-2.92	0.2655	152	0.2774	2613	X-RAY DIFFRACTION	99.82
2.92-3.03	0.2817	135	0.2612	2617	X-RAY DIFFRACTION	99.82
3.03-3.15	0.2678	143	0.244	2613	X-RAY DIFFRACTION	99.89
3.15-3.29	0.2515	139	0.2533	2629	X-RAY DIFFRACTION	99.86
3.29-3.47	0.3005	141	0.2337	2638	X-RAY DIFFRACTION	99.89
3.47-3.68	0.2787	138	0.2275	2651	X-RAY DIFFRACTION	99.5
3.68-3.97	0.2438	142	0.2177	2621	X-RAY DIFFRACTION	98.64
3.97-4.37	0.2298	131	0.2008	2667	X-RAY DIFFRACTION	98.87
4.37-5	0.1742	141	0.1805	2654	X-RAY DIFFRACTION	98.87
5-6.29	0.2334	141	0.2062	2744	X-RAY DIFFRACTION	99.14
6.29-43.63	0.2101	179	0.2031	2889	X-RAY DIFFRACTION	98.97

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	1.48752780831	1.0172136326	-0.352980911765	4.25110910577	-1.89792722974	3.58893078125	-0.153231707871	-0.0328848043694	-0.0749021249534	-0.332887681531	-0.235732833687	-0.483531001514	0.323600257991	0.00248133124083	0.350806388984	0.617464421096	0.080134892088	0.163237054216	0.659925160627	0.164066360798	0.616807770133	-24.7520719344	31.5932443876	18.7374660154
2	4.93308089707	-0.426051142046	-1.70162511322	4.47342429287	0.654399244058	4.92171711006	-0.183793265694	0.718197943756	0.373880982269	-0.61374134747	-0.309046488641	0.142242145377	0.0933148286116	-0.268843317157	0.343074712939	0.61974407676	0.0891944910849	0.0455590476744	0.627279835572	0.190365247798	0.435190689115	-30.2764907986	43.9276371928	14.8749815935
3	1.33154504924	0.179533353414	-0.958720766777	0.362190337553	0.130948483138	1.18881799216	0.0573235691772	0.0886617602204	0.160100691744	-0.529201497835	0.0851145477466	-0.544617348383	0.435024685468	0.349585444928	0.0152594261135	0.941962290006	0.0163298111487	0.168849973016	0.693268015596	0.155748356315	0.679849421476	-9.53514863994	44.1533142035	7.47638366156
4	2.97980124203	-0.317873185402	-1.94749666735	1.43591415867	0.422135205027	1.56737062632	-0.542390053091	-0.0361390620289	-1.28630470887	-0.244648495552	0.225032998767	0.256235253264	0.462061082693	-0.00456667036104	0.272696101034	0.821773825189	0.0179214517126	0.215942731359	0.670225880746	0.181763178727	0.814435550016	-28.0730540112	20.7536184033	21.7388602712
5	3.5573857495	0.547267016834	-0.193214493669	3.70789208207	0.0532869385532	2.40020344286	-0.129684906439	-0.521168587817	-0.700966562252	-0.0391811846611	-0.0245144597858	0.169691501252	0.549423891532	-0.366591556259	0.171311631899	0.738573013529	0.0155761725184	0.147766854411	0.842018213686	0.313673340992	0.829427342193	-35.1880093175	19.2979136424	30.5722224351
6	1.97108786327	-0.838008804911	-0.860402926312	2.31846898203	1.49611607238	1.99957347118	-0.246388790929	0.12212110386	-0.376897518152	-0.205587145906	0.261181137719	-0.137510549505	0.220199736467	-0.0376225600318	-0.0297830741137	0.840383399603	-0.00687106624532	0.264022601969	0.599644667091	0.117840296732	0.686709639404	-10.6823649717	23.6356037393	11.3913903372
7	5.7408472754	-2.13680956224	-2.50701886548	3.24831352333	-0.414507536826	4.26992966388	-0.390077843977	0.416425753121	0.114507477293	-0.173382184096	-0.354316159629	-1.13453324215	0.513600925219	0.746791084371	0.596534518267	0.636433312115	0.0413311952165	-0.01925494712	0.928193837372	0.438226461808	0.957812553249	-8.97756361241	41.2406072265	31.8796017752
8	5.91616637054	-0.239393432045	-1.29868131275	5.83083493258	-2.35326349852	6.07180910182	-0.551331149109	-0.0500033807542	0.708244172031	0.803996664629	-0.392104322975	-0.86619394899	-1.09658585308	0.535586387351	0.815234051634	0.765256753088	-0.0580123520853	-0.299689430446	0.762780951094	0.321052929367	0.801499437514	-17.5096301493	53.0164704514	34.2608951854
9	0.247956022728	0.329526177165	0.682946411531	3.65060982699	-2.26997255416	1.20111329124	-0.349675935172	-0.388951551509	0.142173279729	0.46952057015	-0.150727128795	-0.370419927935	-0.158618707398	0.359649540286	0.205684026053	0.575436943144	0.111445383128	0.0282442998579	0.89526850814	0.276138684436	0.693422051671	-19.0405446713	32.1143266508	40.0280206888
10	1.3250547898	-2.03727611692	1.14086891915	5.82160587433	-1.49842734342	1.90424648427	-0.153924369537	0.108469148656	0.252126043377	-0.380639698763	-0.767858483934	-1.76312548104	0.132156098536	0.964481347129	0.398240957949	0.542805910969	0.0848765027572	0.171130946857	1.24807472333	0.607693757049	1.19835688564	-3.60020236394	33.2500973395	33.9817154799

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 33 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 89 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 90 through 119 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 120 through 172 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 173 through 239 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 382 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 33 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34 through 89 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 90 through 135 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 136 through 383 )

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