PDB-7mcj: Crystal Structure of S-adenosylmethionine-dependent methyltransfe...

ID or keywords:

Entry

Database: PDB / ID: 7mcj

Title

Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with compound 8918

Components

S-adenosylmethionine-dependent methyltransferase UmaA

Keywords

TRANSFERASE / SSGCID / short-chain fatty acid modification / compound 8918 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

lipid biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with compound 8918
Authors: Abendroth, J. / Dranow, D.M. / Kahlert, G. / Scarry, S.M. / Grzegorzewicz, A. / Jackson, M. / Aube, J. / Sherman, D.R. / Gold, B.S. / Nathan, C.F. / Moritz, R.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Apr 2, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 4, 2022	Group: Database references / Category: citation_author
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	7mcj.cif.gz	291.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7mcj.ent.gz	193.6 KB	Display	PDB format
PDBx/mmJSON format	7mcj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mcj_validation.pdf.gz	984.5 KB	Display	wwPDB validaton report
Full document	7mcj_full_validation.pdf.gz	986.8 KB	Display
Data in XML	7mcj_validation.xml.gz	24.1 KB	Display
Data in CIF	7mcj_validation.cif.gz	34.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mc/7mcj ftp://data.pdbj.org/pub/pdb/validation_reports/mc/7mcj	HTTPS FTP

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Related structure data

Related structure data	7l9uS 7lxi S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MytuD.00149.b

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: S-adenosylmethionine-dependent methyltransferase UmaA

B: S-adenosylmethionine-dependent methyltransferase UmaA

hetero molecules

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

1

A: S-adenosylmethionine-dependent methyltransferase UmaA

hetero molecules

defined by author&software
Evidence: gel filtration
34.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: S-adenosylmethionine-dependent methyltransferase UmaA

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.850, 100.850, 49.690
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂
Space group name Hall	P3₂
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3

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Protein , 1 types, 2 molecules AB

#1: Protein	S-adenosylmethionine-dependent methyltransferase UmaA / SAM-dependent methyltransferase UmaA Mass: 34162.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: umaA, Rv0469, LH57_02505 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6MX39, Transferases; Transferring one-carbon groups; Methyltransferases

#1: Protein

S-adenosylmethionine-dependent methyltransferase UmaA / SAM-dependent methyltransferase UmaA

Mass: 34162.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: umaA, Rv0469, LH57_02505 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6MX39, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 6 types, 305 molecules

#2: Chemical	ChemComp-FD7 / N-(2,6-diethylphenyl)-N'-(N-ethylcarbamimidoyl)urea Mass: 262.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₄O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.5 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Optimization condition based on Anatrace/Calibre MCSG1 screen, condition C9: 33% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.0: MytuD.00149.b.B1.PW38903 at 35mg/ml + ...Details: Optimization condition based on Anatrace/Calibre MCSG1 screen, condition C9: 33% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.0: MytuD.00149.b.B1.PW38903 at 35mg/ml + 5mM compound 8918: tray 319823 a10, cryo: 20% EG + 5mM compound: puck hyq3-8

Crystal

Density Matthews: 2.14 Å³/Da / Density % sol: 42.5 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Optimization condition based on Anatrace/Calibre MCSG1 screen, condition C9: 33% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.0: MytuD.00149.b.B1.PW38903 at 35mg/ml + ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 11, 2021

Radiation

Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 52394 / % possible obs: 100 % / Redundancy: 4.66 % / B_iso Wilson estimate: 40.035 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.054 / R_rim(I) all: 0.061 / Χ²: 0.955 / Net I/σ(I): 15.85

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.8-1.85	4.124	0.563	2.23	3862	0.749	0.648	99.9
1.85-1.9	4.727	0.41	3.35	3818	0.88	0.462	100
1.9-1.95	4.77	0.308	4.51	3628	0.932	0.347	100
1.95-2.01	4.775	0.216	6.43	3596	0.961	0.243	100
2.01-2.08	4.79	0.167	8.48	3475	0.972	0.188	100
2.08-2.15	4.784	0.134	10.41	3321	0.983	0.151	100
2.15-2.23	4.777	0.105	13.2	3233	0.988	0.119	100
2.23-2.32	4.742	0.085	16.21	3088	0.991	0.095	100
2.32-2.43	4.731	0.076	18.19	2974	0.993	0.085	100
2.43-2.55	4.699	0.069	20.01	2855	0.994	0.078	100
2.55-2.68	4.687	0.06	22.78	2726	0.994	0.068	100
2.68-2.85	4.627	0.055	24.36	2552	0.995	0.063	100
2.85-3.04	4.621	0.052	26.27	2412	0.995	0.059	100
3.04-3.29	4.609	0.051	27.62	2248	0.995	0.057	100
3.29-3.6	4.595	0.048	28.86	2061	0.996	0.054	100
3.6-4.02	4.601	0.047	29.36	1866	0.996	0.053	100
4.02-4.65	4.611	0.045	29.5	1637	0.996	0.05	100
4.65-5.69	4.638	0.044	29.68	1383	0.995	0.05	100
5.69-8.05	4.617	0.043	29.53	1081	0.997	0.048	100
8.05-50	4.343	0.041	28.59	578	0.995	0.047	98.3

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19 dev 4175	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: apo structure, PDB entry 7L9U

7l9u

Resolution: 1.8→43.19 Å / SU ML: 0.2595 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.3813
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2205	2091	3.99 %	0
R_work	0.1887	50280	-	-
obs	0.1901	52371	99.97 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 41.85 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→43.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4355	0	62	294	4711

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	4513
X-RAY DIFFRACTION	f_angle_d	0.7371	6091
X-RAY DIFFRACTION	f_chiral_restr	0.0481	656
X-RAY DIFFRACTION	f_plane_restr	0.0059	813
X-RAY DIFFRACTION	f_dihedral_angle_d	13.5752	1636

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 (%)
1.8-1.84	0.3143	106	0.2926	3408	X-RAY DIFFRACTION	99.91
1.84-1.89	0.2859	162	0.2466	3304	X-RAY DIFFRACTION	100
1.89-1.94	0.2642	130	0.2249	3375	X-RAY DIFFRACTION	100
1.94-2	0.3088	148	0.2029	3327	X-RAY DIFFRACTION	100
2-2.06	0.2232	130	0.212	3350	X-RAY DIFFRACTION	100
2.06-2.13	0.231	153	0.2089	3337	X-RAY DIFFRACTION	100
2.13-2.22	0.2396	134	0.1995	3354	X-RAY DIFFRACTION	100
2.22-2.32	0.2523	143	0.1925	3366	X-RAY DIFFRACTION	100
2.32-2.44	0.2323	142	0.221	3372	X-RAY DIFFRACTION	100
2.44-2.6	0.2329	157	0.2181	3326	X-RAY DIFFRACTION	100
2.6-2.8	0.2265	110	0.2009	3386	X-RAY DIFFRACTION	100
2.8-3.08	0.2388	150	0.2104	3331	X-RAY DIFFRACTION	100
3.08-3.52	0.2206	123	0.1829	3392	X-RAY DIFFRACTION	100
3.52-4.43	0.1912	134	0.1573	3339	X-RAY DIFFRACTION	100
4.44-43.19	0.1986	169	0.1667	3313	X-RAY DIFFRACTION	99.69

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	0.0257157622951	-0.244158787553	0.280789036089	1.91151774614	-1.157125135	0.583906581568	-0.181489924702	-0.958480129717	-0.650142342065	0.543500338799	-0.00795035817146	-0.989767890619	0.539029930735	0.971808998938	0.110244029392	0.551301888792	0.145905513587	0.00761413590871	0.397896705008	0.149293888554	0.69023164818	13.9244958942	12.2207809829	-11.208746071
2	4.74366065137	-0.945258324831	-2.30119932148	1.18528434599	1.66765716046	5.15161366	0.0876987971449	0.050031243264	-0.116163925167	-0.0407937979151	-0.047080634875	0.0192600618077	-0.428808751163	-0.0785115007424	-0.0398202242057	0.282001028302	-0.00697993009467	-0.0113565410468	0.226273996528	0.0230865035171	0.267257904609	1.92686655138	33.276242277	-7.39344817525
3	3.61756248369	0.483481308231	-0.131810676157	2.02414588014	0.284669826812	3.00559386794	-0.0757428668475	-0.526331758115	-0.572301295424	0.266513253567	-0.0139616852956	-0.130459675349	0.0275358849374	0.247584082526	0.117101634708	0.284307424276	0.0042728188859	-0.00699965236198	0.353240636836	0.146404002112	0.276308921915	8.00241058756	28.0156596851	7.38412983777
4	1.78051182726	-1.03206431256	0.12521978443	2.54874508732	0.0277486616975	3.69311294328	-0.352303202989	-0.825087419975	-1.22031302579	0.398751891554	-0.175010734876	0.784474771398	0.443003403484	0.236762388445	0.305803770795	0.381132871256	0.0360806960841	0.1654871451	0.568462646384	0.281622670051	0.619562610651	-5.25777183106	21.4752778024	9.79991278929
5	1.92319710649	0.200178100612	-2.41881100877	2.44761387807	0.989782062161	3.94888601561	-0.455207930446	0.0633800296032	-1.28277736164	0.259314985222	-0.201701883919	1.03548642932	0.564384689728	-0.56903814388	0.501130350366	0.417545651802	-0.0989253585224	-0.0368065598558	0.433276605648	-0.166108818344	1.07024247074	-11.707468996	11.4750788005	-14.1025214716
6	1.91965255017	-0.65410618489	0.563540522134	2.17412586002	0.354934192524	1.96304957369	-0.372302351798	-0.423924529335	-0.966234532201	0.487327764247	-0.125761449772	0.571540177585	0.516371127813	0.0124489974338	0.460414480552	0.385644999026	0.0398104023932	0.198055776984	0.3204051638	0.107289760698	0.666293164854	-12.039363268	21.4123187607	3.87384292047
7	3.14494844374	0.892704958501	-0.729036535591	2.77555617242	0.123643080113	3.53695415595	0.051749617905	0.278939344749	-0.899322629851	-0.269869239738	-0.157117070129	0.0267254459185	-0.061348237426	0.00462586961889	0.0974428664556	0.203348689027	0.024339604555	-0.0556798173052	0.136056860206	-0.0236432662047	0.305307922943	6.73995598763	22.752845455	-18.3321769356
8	4.268882615	-0.843651918461	-2.25248191827	1.97788804217	1.67833387482	3.97992382098	-0.143814292071	0.131722553972	-0.815192367468	-0.100854915086	0.0477485734099	0.193428407351	0.195203272574	0.113930643586	0.137031769816	0.296735357711	0.0013817106261	-0.0431048632197	0.218850383496	0.0158292559589	0.498688487694	-2.00700971221	18.9968683094	-12.3945872574
9	2.52365712339	-0.474122042504	-1.07300000774	2.57631815661	1.20998225596	4.88349783896	0.0840701042994	-0.0696168494742	0.0488465178338	0.330605789248	-0.00676164291342	0.293406588235	-0.0137444989001	-0.121311910983	-0.125234293618	0.257749557241	-0.0236324158557	0.0334761932893	0.165296508084	0.0346756363729	0.265998471341	-26.9800525236	46.1304285596	7.96109686533
10	2.47989544622	-0.255943333586	-0.842996845877	4.53033764294	0.0921104286221	2.43656775404	0.13688529634	0.367330139834	-0.08231056148	-0.29329728104	-0.125253351766	0.473084089322	-0.124398802368	-0.148732028218	-0.00968806530072	0.294071625839	0.035889012719	-0.057673721294	0.291023638677	-0.0114851467279	0.259055562406	-29.5302723954	50.4298693479	-7.3711559236
11	3.45908711296	1.49668601087	-0.757252258473	3.51601078178	0.0526228650035	2.99423767664	-0.128785545664	0.63037989176	-0.379285829484	-0.429773546182	-0.113338013051	0.614475679307	-0.0789259199962	-0.713449722306	0.237558425861	0.351496883658	0.0327418863359	-0.0586697212603	0.376812807167	-0.123759915864	0.399032689118	-29.9837164061	38.8980776934	-9.3571839387
12	3.5029096655	-0.659773757742	-0.83095940376	4.10262246174	-0.309375811415	2.58840100774	-0.117266467115	0.179950169417	-0.903512702671	-0.28305762739	-0.149210287733	0.620087511073	0.418416770122	-0.0601975255086	0.211853031551	0.307834561596	-0.0141646641487	0.0459129237363	0.247569947399	-0.124417466649	0.61314589058	-26.7151923345	28.4538113454	-2.8788633959
13	5.33834934545	-2.91252471695	-3.01624969757	6.68236706218	1.83244176972	5.05294078194	-1.00489544874	-0.643044236906	-1.83671527999	0.903090759463	0.411550888005	1.73377735685	1.03420866929	-0.823816158437	0.476052968612	0.558422630963	-0.0929489736894	0.264142945595	0.386665506951	-0.04221235338	0.917223626115	-39.7718280384	26.221335486	15.8756806828
14	4.383017178	-1.59522924856	-2.55884456613	1.37973582053	0.29957527235	5.02052384969	-0.233089001791	0.225155528152	-1.12120082963	0.057345920526	-0.176303836386	0.813981900794	0.433791846642	-0.372422856077	0.310303195281	0.345994361856	-0.0465424478982	0.0845946652595	0.334736991527	-0.180709105358	0.916597254347	-29.933086775	25.9773080122	-2.70944829086
15	2.06214123036	-0.465193713917	-0.988641513978	3.31360761632	0.188790222499	1.20917278067	-0.0542439685378	-0.170094898096	-0.414107144627	0.720930945056	-0.14517090092	0.524021463268	0.253368823613	-0.1439282131	0.221930889911	0.337223622836	-0.0595275435139	0.0535057752136	0.232676815613	-0.00848808246311	0.367799896083	-30.1526283208	37.6147728299	11.6141030427

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 6 through 24 )	A	A	6 - 24	1 - 17
2	2	chain 'A' and (resid 25 through 59 )	A	A	25 - 59	18 - 52
3	3	chain 'A' and (resid 60 through 142 )	A	A	60 - 142	53 - 135
4	4	chain 'A' and (resid 143 through 170 )	A	A	143 - 170	136 - 163
5	5	chain 'A' and (resid 171 through 197 )	A	A	171 - 197	164 - 190
6	6	chain 'A' and (resid 198 through 227 )	A	A	198 - 227	191 - 217
7	7	chain 'A' and (resid 228 through 254 )	A	A	228 - 254	218 - 244
8	8	chain 'A' and (resid 255 through 286 )	A	A	255 - 286	245 - 276
9	9	chain 'B' and (resid 13 through 59 )	B	G	13 - 59	1 - 47
10	10	chain 'B' and (resid 60 through 124 )	B	G	60 - 124	48 - 112
11	11	chain 'B' and (resid 125 through 142 )	B	G	125 - 142	113 - 130
12	12	chain 'B' and (resid 143 through 184 )	B	G	143 - 184	131 - 172
13	13	chain 'B' and (resid 185 through 197 )	B	G	185 - 197	173 - 185
14	14	chain 'B' and (resid 198 through 217 )	B	G	198 - 217	186 - 205
15	15	chain 'B' and (resid 218 through 286 )	B	G	218 - 286	206 - 274

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