PDB-8tjj: SAM-dependent methyltransferase RedM bound to SAM

ID or keywords:

Entry

Database: PDB / ID: 8tjj

Title

SAM-dependent methyltransferase RedM bound to SAM

Components

RedM

Keywords

BIOSYNTHETIC PROTEIN / methyltransferase / indolocarbazole / conformational change

Function / homology

Function and homology information

O-methyltransferase activity
Similarity search - Function

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.82 Å

Authors

Daniel-Ivad, P. / Ryan, K.S.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Structure of methyltransferase RedM that forms the dimethylpyrrolinium of the bisindole reductasporine.
Authors: Daniel-Ivad, P. / Ryan, K.S.

History

Deposition	Jul 22, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tjj.cif.gz	591.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8tjj.ent.gz	433.1 KB	Display	PDB format
PDBx/mmJSON format	8tjj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tjj_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8tjj_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8tjj_validation.xml.gz	59.1 KB	Display
Data in CIF	8tjj_validation.cif.gz	88.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/8tjj ftp://data.pdbj.org/pub/pdb/validation_reports/tj/8tjj	HTTPS FTP

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Related structure data

Related structure data	8tjiC 8tjkC 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: RedM

B: RedM

C: RedM

D: RedM

hetero molecules

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

1

A: RedM

D: RedM

hetero molecules

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

2

B: RedM

C: RedM

hetero molecules

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

Unit cell

Length a, b, c (Å)	113.860, 58.780, 113.920
Angle α, β, γ (deg.)	90.000, 103.110, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	RedM Mass: 37781.816 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: environmental DNA Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: redM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7G196

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Non-polymers , 6 types, 1255 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1233 / 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: 2.4 Å³/Da / Density % sol: 48.7 % / Description: plates, occasionally clustered at one end
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2-0.3 M ammonium sulphate, 0.1 M MES pH 6.5, 18-24 % PEG MME 5000, 13-16 mg.mL RedM PH range: 6-7 / Temp details: ambient

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9796 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 1.82→89.2 Å / Num. obs: 125933 / % possible obs: 95.9 % / Redundancy: 6.5 % / B_iso Wilson estimate: 21.01 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.146 / R_pim(I) all: 0.061 / R_rim(I) all: 0.159 / Net I/σ(I): 9.5
Reflection shell	Resolution: 1.82→1.85 Å / Redundancy: 6.7 % / R_merge(I) obs: 1.215 / Num. unique obs: 6228 / CC_1/2: 0.367 / R_pim(I) all: 0.501 / R_rim(I) all: 1.316 / % possible all: 96.7

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
Blu-Ice		data collection
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing
PHENIX	1.19_4092	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.82→45.64 Å / SU ML: 0.2135 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2175	6531	5.19 %
R_work	0.1753	119375	-
obs	0.1775	125906	95.72 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→45.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9777	0	179	1233	11189

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0053	10188
X-RAY DIFFRACTION	f_angle_d	0.7659	13830
X-RAY DIFFRACTION	f_chiral_restr	0.0471	1558
X-RAY DIFFRACTION	f_plane_restr	0.0067	1789
X-RAY DIFFRACTION	f_dihedral_angle_d	12.509	3663

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 (%)
1.82-1.84	0.361	203	0.3076	4020	X-RAY DIFFRACTION	96.17
1.84-1.86	0.3181	203	0.2942	3964	X-RAY DIFFRACTION	97.36
1.86-1.89	0.313	216	0.2825	3990	X-RAY DIFFRACTION	95.94
1.89-1.91	0.3192	218	0.2702	3983	X-RAY DIFFRACTION	96.84
1.91-1.94	0.2691	229	0.2552	3993	X-RAY DIFFRACTION	96.66
1.94-1.96	0.2936	221	0.2423	4005	X-RAY DIFFRACTION	96.29
1.96-1.99	0.2727	216	0.2328	3959	X-RAY DIFFRACTION	97.05
1.99-2.02	0.2965	232	0.2337	3996	X-RAY DIFFRACTION	95.94
2.02-2.05	0.2719	190	0.2272	3554	X-RAY DIFFRACTION	86.81
2.05-2.09	0.2577	194	0.2074	3834	X-RAY DIFFRACTION	92.6
2.09-2.12	0.2455	218	0.189	4068	X-RAY DIFFRACTION	97.52
2.12-2.16	0.2626	176	0.1919	4106	X-RAY DIFFRACTION	97.52
2.16-2.2	0.2238	178	0.1831	3962	X-RAY DIFFRACTION	95.86
2.2-2.25	0.2282	221	0.1796	4110	X-RAY DIFFRACTION	98.12
2.25-2.3	0.2162	239	0.1782	3957	X-RAY DIFFRACTION	97.04
2.3-2.35	0.232	235	0.1727	3976	X-RAY DIFFRACTION	96.23
2.35-2.41	0.2095	242	0.1659	4044	X-RAY DIFFRACTION	97.68
2.41-2.47	0.2321	201	0.1661	3761	X-RAY DIFFRACTION	90.56
2.47-2.55	0.2018	211	0.1611	3796	X-RAY DIFFRACTION	91.71
2.55-2.63	0.1905	217	0.1664	4067	X-RAY DIFFRACTION	98.26
2.63-2.72	0.2413	237	0.1721	4104	X-RAY DIFFRACTION	98.46
2.72-2.83	0.2227	179	0.1731	4008	X-RAY DIFFRACTION	95.72
2.83-2.96	0.2195	226	0.1671	4057	X-RAY DIFFRACTION	97.83
2.96-3.12	0.2064	206	0.1729	4093	X-RAY DIFFRACTION	97.59
3.12-3.31	0.2215	228	0.1643	3634	X-RAY DIFFRACTION	88.01
3.31-3.57	0.2088	254	0.1569	4136	X-RAY DIFFRACTION	98.87
3.57-3.92	0.1809	255	0.1428	4077	X-RAY DIFFRACTION	98.01
3.92-4.49	0.163	224	0.1273	4081	X-RAY DIFFRACTION	97.38
4.49-5.66	0.1617	232	0.1432	3884	X-RAY DIFFRACTION	91.88
5.66-45.64	0.2039	230	0.175	4156	X-RAY DIFFRACTION	95.7

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	1.70229541243	-0.700390439497	-0.00472869505522	1.12779126009	-0.664828420388	2.64547416539	0.119790814843	0.560023212721	0.383156136927	-0.142713217107	-0.239941230842	-0.240717521246	-0.2987500586	0.0624027850904	0.124639735442	0.265196828602	0.0505279687841	0.0195681579231	0.292646514663	0.149586491041	0.234412831927	21.8060637803	23.2457900894	77.8731834335
2	1.0226013449	0.226282183082	-1.57413277244	0.78830280879	-0.826712402957	3.80690971751	-0.0209559806891	0.328313413074	0.187097613087	-0.14547110188	0.461806643816	0.0204264997394	-0.265493285579	-1.2746263046	-0.199818115859	0.32513134398	0.097577318182	-0.00958453782719	0.687988516237	0.128786810258	0.184748171057	8.52875510919	29.2413826254	53.1501158455
3	0.541513752855	-0.110151977933	-0.0759054463485	2.57330314558	0.268615502727	0.523195203425	0.0107149647998	-0.016043981794	0.0224625121407	0.109649895583	0.0032879695526	-0.0557681583498	-0.0293163513076	0.0365081744511	-0.0221141948026	0.0984292436984	-0.0103997638227	0.002293405772	0.0831069575099	0.0028783026808	0.0875056269791	7.48518526521	31.2152893141	130.74678782
4	1.3243816295	-0.0902923157663	0.0301423750518	0.940196881999	1.43836164285	3.37725572812	0.0379253500159	-0.26351745833	-0.0148836706168	0.479004069406	0.169898237913	-0.150522558219	0.464091105234	0.401095536967	-0.13614826684	0.393150170409	0.0708755218897	-0.0581142220937	0.211312830235	0.00705088159159	0.186534472438	10.3299904962	13.7398497305	153.311558541
5	0.20139568403	0.193774571349	-0.189278671785	1.72665938599	0.48714775985	0.701405222133	0.0123916709133	-0.0448701113483	0.0400909874108	0.35955651843	-0.0018699937907	0.185873842944	0.0542023829157	0.0350622779393	0.00409163190947	0.152216703272	-0.0126924147416	0.00368973872113	0.107173233395	0.0129329769047	0.122876355555	-0.759636767359	21.536754487	131.961650785
6	0.303611437181	-0.245119592161	0.241693262761	0.421222876984	-0.028489933634	0.689933781276	-0.0617079790464	0.0269118074258	-0.30313927331	0.0271231290412	0.0327656133403	0.163630010021	0.209134792756	-0.0914181034555	-0.0337293104509	0.165958369465	-0.0200777795012	0.0219574273464	0.112245570677	-0.0156525395475	0.213405575775	-5.53470741188	0.305503028756	125.975559508
7	0.447320283909	-0.314227379841	0.540675187154	0.501444202098	-0.359351447728	1.26947135252	-0.0644915219006	-0.154755996523	0.0715405174949	0.291498781842	0.0194209482823	0.296087432999	0.139603492625	-0.207208394455	-0.0283900025032	0.148915229533	-0.0155012494285	0.0405614719473	0.106591687759	-0.00861519169667	0.167196382838	-8.0681786116	7.78514361913	133.021658806
8	0.719142250855	1.04210113562	-0.369882886305	1.78010139962	-0.288618837338	0.555948495591	-0.14209009173	0.172872027398	-0.118160879077	-0.240552775855	0.12730428002	-0.0596534179688	0.0635652392221	-0.105665562572	-0.00810875728531	0.139554880762	0.00587117590418	-0.00874881813042	0.108753015718	0.00111089850192	0.133873127107	0.881989538971	20.0730072739	116.057082831
9	1.32979410086	0.121049505333	-0.12724570493	1.30634034567	0.689647276587	1.28840020212	-0.0164524093958	-0.120207730134	-0.158537427662	0.0722231720306	0.0615812811976	0.260586280267	0.0773485220154	-0.152127114796	-0.0291396471892	0.152127831726	-0.0172216193289	-0.0247705380614	0.135962447216	0.0149905995079	0.144307983688	-11.715505551	22.6519341084	108.788520566
10	3.48228743156	0.00476318100635	0.37015839773	1.8459772168	0.0415532791496	2.17974551281	-0.0248957249631	0.272132662913	-0.182743265099	-0.325085875971	-0.0384765972959	0.213559084274	0.011932221047	0.115056759079	0.0422266442441	0.160659467125	0.0219852271059	-0.0613965799236	0.224159860652	-0.01031078032	0.171241096283	-15.9937803264	31.5086812689	95.7813567473
11	1.51445480228	-0.0512660900724	0.759004538583	0.696676167011	0.626349212298	1.53646900883	-0.0713171752819	0.178143352887	0.234559586971	-0.0886014670406	0.0844684659698	0.175797533821	-0.247848895354	0.0542223795207	0.0389586413065	0.147491933905	-0.0292819176385	-0.0526002598137	0.126268018438	0.0450197181992	0.217296707322	-8.6611486097	42.8564692354	107.383177015
12	1.05466864641	0.164121899898	-0.074593283253	0.591089742793	-0.267026976423	1.11741553657	-0.0527722550168	0.0290411051659	0.215050748801	-0.122823069023	-0.0186821618787	-0.00945429436949	-0.0619075699593	-0.0529547117748	0.0746190410236	0.140397039156	-0.0247167516588	-0.0281162407441	0.0775907477353	0.00322372435446	0.162526972903	-2.83732646124	40.8083532554	114.091336714
13	1.19455442718	-0.301443977171	-0.45264737826	0.814400407209	0.982067807596	1.19181572765	-0.105023468738	-0.0203224958611	0.273471815891	-0.280344804856	-0.0701542098835	0.216383082911	0.017229976612	-0.217609276594	0.243929696562	0.179421917142	-0.00238045994474	-0.0774654039791	0.163492294351	0.0109742253028	0.285022748974	-16.7946504525	43.6003415237	110.36637245
14	1.58872180475	0.503815004113	0.306356518231	1.27644642297	-0.760075660081	1.91057671905	-0.245916921256	0.84514853309	-0.237335154986	-0.340378227611	0.395915814004	0.156108188333	0.598629585631	-1.10563690727	-0.382345620377	0.280664914804	-0.148202645756	-0.0614685584668	0.752527406285	0.0434909949491	0.174419856554	-0.645995978813	10.4798274123	77.0681722799
15	2.14196630067	0.637550601247	-0.510541399994	0.383493981542	-0.1762199263	1.44051274408	0.0662643965303	0.262146607702	0.159827394265	0.195798523132	0.0407477892536	-0.0852756813708	-0.126544474445	-0.2361342731	-0.0716677036628	0.235173293368	0.0572120020618	-0.0180312172546	0.192045251689	0.0404897418613	0.195900223505	8.84186208177	18.9634243478	94.931589699
16	1.77961431528	1.33769739172	-0.8562155544	2.76979206572	-0.454988379268	0.918564871574	-0.0646068256559	0.000293940745559	-0.0383878182054	-0.0815180293297	-0.00179928949569	-0.0138360192687	0.0532613583021	0.00786254960356	0.0666873177882	0.131099377488	-0.000510046324195	-0.00898686610888	0.0935399725382	0.035072708027	0.139927734979	17.6897463477	-0.120060791001	109.86324925
17	1.793561761	-0.429922600708	0.369274790362	1.49641006269	-1.22856847588	1.92107421532	-0.00387973849542	0.0260237716544	-0.211338494335	-0.250717388924	-0.0653922102069	-0.157541218377	0.233691519483	0.0721622042954	0.0289046973702	0.144121354387	-0.00932781007946	0.0178109107347	0.0910045391201	0.0230918895591	0.175310099158	28.8289865076	4.91554658964	98.2496724114

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 12 through 160 )	A	A	12 - 160	1 - 134
2	2	chain 'A' and (resid 161 through 344 )	A	A	161 - 344	135 - 318
3	3	chain 'B' and (resid 13 through 149 )	B	E	13 - 149	2 - 125
4	4	chain 'B' and (resid 150 through 344 )	B	E	150 - 344	126 - 320
5	5	chain 'C' and (resid 10 through 36 )	C	M	10 - 36	2 - 28
6	6	chain 'C' and (resid 37 through 62 )	C	M	37 - 62	29 - 54
7	7	chain 'C' and (resid 63 through 81 )	C	M	63 - 81	55 - 73
8	8	chain 'C' and (resid 82 through 146 )	C	M	82 - 146	74 - 132
9	9	chain 'C' and (resid 147 through 171 )	C	M	147 - 171	133 - 157
10	10	chain 'C' and (resid 172 through 244 )	C	M	172 - 244	158 - 230
11	11	chain 'C' and (resid 245 through 291 )	C	M	245 - 291	231 - 277
12	12	chain 'C' and (resid 292 through 322 )	C	M	292 - 322	278 - 308
13	13	chain 'C' and (resid 323 through 344 )	C	M	323 - 344	309 - 330
14	14	chain 'D' and (resid 12 through 101 )	D	W	12 - 101	1 - 90
15	15	chain 'D' and (resid 102 through 160 )	D	W	102 - 160	91 - 145
16	16	chain 'D' and (resid 161 through 270 )	D	W	161 - 270	146 - 255
17	17	chain 'D' and (resid 271 through 344 )	D	W	271 - 344	256 - 329

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 1255 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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Yorodumi