PDB-8tji: SAM-dependent methyltransferase RedM, apo

ID or keywords:

Entry

Database: PDB / ID: 8tji

Title

SAM-dependent methyltransferase RedM, apo

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: 1.73 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	8tji.cif.gz	306.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8tji.ent.gz	218.8 KB	Display	PDB format
PDBx/mmJSON format	8tji.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tji_validation.pdf.gz	450 KB	Display	wwPDB validaton report
Full document	8tji_full_validation.pdf.gz	450.7 KB	Display
Data in XML	8tji_validation.xml.gz	31.7 KB	Display
Data in CIF	8tji_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/8tji ftp://data.pdbj.org/pub/pdb/validation_reports/tj/8tji	HTTPS FTP

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Related structure data

Related structure data	8tjjC 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

Deposited unit

A: RedM

B: RedM

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.950, 71.610, 145.000
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	RedM Mass: 37781.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: environmental DNA Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: redM / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7G196
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H₂O
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: 2.08 Å³/Da / Density % sol: 40.8 % / Description: plates
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 % PED MME 5000, 13-16 mg/mL RedM, 1:1 drop ratio, 2-4 uL total 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: 1.73→72.5 Å / Num. obs: 67710 / % possible obs: 99.4 % / Redundancy: 11.5 % / B_iso Wilson estimate: 17.89 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.019 / R_rim(I) all: 0.067 / Net I/σ(I): 23.6
Reflection shell	Resolution: 1.73→1.76 Å / R_merge(I) obs: 0.241 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 3483 / CC_1/2: 0.96 / R_pim(I) all: 0.101 / R_rim(I) all: 0.263 / % possible all: 95

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→47.1 Å / SU ML: 0.1884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1992	3390	5.05 %
R_work	0.1669	63778	-
obs	0.1685	67168	98.6 %

Solvent computation

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

Displacement parameters

B_iso mean: 21.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→47.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4805	0	36	855	5696

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	4964
X-RAY DIFFRACTION	f_angle_d	0.682	6730
X-RAY DIFFRACTION	f_chiral_restr	0.0452	753
X-RAY DIFFRACTION	f_plane_restr	0.0064	878
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1404	1807

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 (%)
1.73-1.75	0.2506	136	0.2181	2494	X-RAY DIFFRACTION	94.13
1.75-1.78	0.229	143	0.1982	2566	X-RAY DIFFRACTION	97.2
1.78-1.81	0.2308	146	0.1953	2635	X-RAY DIFFRACTION	99.57
1.81-1.84	0.219	144	0.1856	2690	X-RAY DIFFRACTION	99.86
1.84-1.87	0.2169	127	0.1789	2639	X-RAY DIFFRACTION	99.93
1.87-1.9	0.2525	130	0.1895	2634	X-RAY DIFFRACTION	97.88
1.9-1.94	0.2891	117	0.2566	2434	X-RAY DIFFRACTION	90.36
1.94-1.98	0.2304	126	0.1731	2651	X-RAY DIFFRACTION	99.86
1.98-2.02	0.2082	133	0.1729	2643	X-RAY DIFFRACTION	99.32
2.02-2.07	0.2149	145	0.1664	2666	X-RAY DIFFRACTION	98.74
2.07-2.12	0.2046	129	0.1663	2655	X-RAY DIFFRACTION	99.64
2.12-2.18	0.1899	125	0.1729	2679	X-RAY DIFFRACTION	99.82
2.18-2.24	0.2396	140	0.1771	2642	X-RAY DIFFRACTION	97.55
2.24-2.32	0.2195	145	0.184	2607	X-RAY DIFFRACTION	97.38
2.32-2.4	0.2231	143	0.1659	2647	X-RAY DIFFRACTION	99.39
2.4-2.5	0.2026	148	0.1632	2646	X-RAY DIFFRACTION	98.94
2.5-2.61	0.1778	137	0.1621	2692	X-RAY DIFFRACTION	99.51
2.61-2.75	0.2157	139	0.1698	2703	X-RAY DIFFRACTION	99.86
2.75-2.92	0.2003	130	0.1686	2701	X-RAY DIFFRACTION	99.89
2.92-3.14	0.1984	186	0.1596	2667	X-RAY DIFFRACTION	99.23
3.14-3.46	0.1792	167	0.1542	2684	X-RAY DIFFRACTION	99.34
3.46-3.96	0.1604	146	0.1401	2736	X-RAY DIFFRACTION	99.9
3.96-4.99	0.1571	157	0.1388	2759	X-RAY DIFFRACTION	99.42
4.99-47.1	0.2125	151	0.1812	2908	X-RAY DIFFRACTION	99.58

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	8.39104985168	-2.22627274048	1.23318862556	2.50275135949	-0.392619159864	1.64501349291	0.122488265242	0.131479839309	0.131999756457	-0.192727924819	-0.138524290304	-0.26948671591	0.120423529893	0.0748085356901	-0.0218036849044	0.108648825944	-0.0270625336125	0.0458716609545	0.149731477101	0.0203035441352	0.129943002528	7.25614913136	35.564124104	-21.2100705352
2	1.70749127832	0.438277332112	-0.139778904841	1.45582366273	-0.196621009889	1.91874740022	-0.0733441098827	0.0763847735119	0.0302879396632	-0.120981647185	0.108947943349	0.265570883522	0.0292197804976	-0.550757732572	-0.0169598784376	0.0807832670322	0.0103410151738	-0.00252456346174	0.239623594077	-0.00393931434887	0.163508253634	-7.9376949686	43.2091281241	-28.1461289386
3	1.42413525137	-1.24356656043	0.136061041247	5.19827593027	-4.65563090044	5.19081476777	0.0172569833563	-0.0571739657859	0.101435766488	0.280894589236	0.0891655688593	0.219826335145	-0.142163622101	-0.100390004286	-0.069440984115	0.0991991807718	-0.0282740269952	0.0444910921064	0.122542316306	-0.0412676133158	0.12460978818	1.22605970663	27.2229042835	-5.32245986861
4	6.17945765463	2.48661663428	1.39032834062	5.76009415273	3.80567533332	3.40002500886	0.263222106157	-0.430734044002	0.745867689229	0.068116323708	-0.307606733468	0.314950046378	-0.94145681012	-0.494378754772	0.100120281405	0.34868873887	0.0568716589552	0.043380017121	0.213356552907	0.0305673326743	0.207129122977	-13.3252743813	16.7976926345	-28.903802518
5	2.05653324195	-0.353964678859	0.0561261418307	1.29356810616	0.0808423030022	3.11230900955	0.0819670496049	0.0362080991467	0.110478221486	-0.0420859842199	-0.0453304920209	0.0909825827735	-0.0265738128438	-0.425758066591	-0.0328925892345	0.0769439496201	-0.0291691565528	0.00781579693683	0.133210951124	-0.00411664555796	0.116141209147	-23.7218595307	10.059939362	-20.8610357829
6	2.006608011	1.60464406215	0.345151388856	2.20803823808	0.821843950994	0.856766855237	0.0656037521532	-0.0226157287312	-0.0931042015477	0.00206062002927	-0.00631263457492	-0.0645890040028	0.174146439403	0.0225992894919	-0.0388850233034	0.110518267084	-0.00201777515572	-0.0151358636999	0.0803633042341	0.00399164819876	0.0782881177536	-4.49092620805	8.41196908989	-15.255292169
7	2.94818779686	3.13369053425	-1.70770067117	5.82148475592	-3.90691633911	2.77166739107	0.0156791385211	0.126308218719	-0.335816036009	-0.0915439986297	-0.0285960543317	-0.174895327155	0.29454330852	0.0987407953405	-0.0152798957532	0.162465684028	0.0161502921329	-0.0157884184155	0.0751561397729	-0.0265858528369	0.116313007114	-5.84682563775	3.06303050471	-24.6005382298
8	8.14176762962	-1.48796195498	7.45235260987	1.92203371682	-1.67247431214	8.12333702054	0.0571313334951	0.143702333293	-0.00279144233515	-0.269149434144	-0.0510033631541	0.0899719329537	0.306252674535	0.0606411614877	-0.0147652228715	0.105917412851	-0.0213314278632	0.0437887286164	0.0794788094489	-0.0148874601604	0.155781118424	4.27004477882	29.9805651826	-20.3785027812
9	1.47567405763	0.00783837191049	-0.0412676708431	0.992992761701	0.0734293289514	1.62788414604	0.00740400107798	0.0327059671478	-0.0375748652395	-0.0339325002135	-0.0290320101118	-0.279515974091	0.0904518844708	0.174354658123	0.0267911216778	0.0652648369327	0.0143202462163	0.0137357635915	0.129018235891	-0.0153648729221	0.141814863566	17.8520902201	23.0521157923	-10.2582024144
10	2.32496933389	-0.777647286067	0.068189129655	3.96996002933	0.449343986904	0.947086725775	-0.0058289496581	-0.304169783593	-0.0571685466817	0.408830745464	-0.0503247180422	0.197202443046	-0.154239548235	-0.420427702422	0.0420109972322	0.15052560261	0.0215510516805	0.0498485530088	0.186890675114	-0.00243523259464	0.104679480086	0.399171535474	46.9738086699	-10.5452322107
11	4.30944132304	3.46303110856	-4.11296211454	4.64154249952	-5.3945247492	9.85030036063	0.240912580311	-0.350190995189	-0.248784728685	0.412099417547	-0.0950785010718	-0.0460797018207	-0.00846258060934	0.119641313784	0.0157731329779	0.298437732256	0.0454150360242	-0.0733814437051	0.236832502811	-0.0243003978127	0.341587970444	24.5239887244	44.0694130694	-14.3548404341
12	3.64879471938	0.447792947886	-0.0347468157542	2.54105755075	0.207434374746	2.70133617436	0.0648595022981	-0.307133303308	-0.205617249253	0.398175212782	-0.0392931793532	-0.351145430679	0.0694266429507	0.174088763331	-0.0216122523919	0.180466914186	-0.0432328637117	-0.0646717454079	0.149750763219	-0.0117544148402	0.174936191777	32.3013634069	57.9531094697	-15.4712433183
13	2.27780355691	1.28057521512	-0.233706861432	1.45177667787	-0.021541851737	0.148789593011	-0.00823656736873	0.033877605801	0.118777660501	0.0171140133131	0.0260315932259	0.0352502357753	-0.118333254069	0.0593764599163	-0.0217343181187	0.109639847484	-0.00191359359561	-0.0116671172452	0.076892317037	-0.00134243824997	0.090619413446	14.4107088574	58.041284666	-24.180847022
14	3.38933170464	0.605032483939	0.355338711631	8.49070027521	1.07765110539	2.6614675736	-0.0342066012867	0.280458307797	-0.182810497779	-0.333122509456	0.0464707554292	0.0428232260763	-0.0650647336395	0.180190526146	-0.00511061722835	0.126097353057	-0.0217907694562	-0.0147085287561	0.152590128141	-0.00481802135611	0.10664769874	22.0198580029	57.4902490468	-30.9901745846

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 35 )	A	A	12 - 35	1 - 24
2	2	chain 'A' and (resid 36 through 111 )	A	A	36 - 111	25 - 100
3	3	chain 'A' and (resid 112 through 130 )	A	A	112 - 130	101 - 119
4	4	chain 'A' and (resid 157 through 171 )	A	A	157 - 171	120 - 134
5	5	chain 'A' and (resid 172 through 244 )	A	A	172 - 244	135 - 207
6	6	chain 'A' and (resid 245 through 322 )	A	A	245 - 322	208 - 285
7	7	chain 'A' and (resid 323 through 344 )	A	A	323 - 344	286 - 307
8	8	chain 'B' and (resid 12 through 35 )	B	B	12 - 35	1 - 24
9	9	chain 'B' and (resid 36 through 111 )	B	B	36 - 111	25 - 100
10	10	chain 'B' and (resid 112 through 135 )	B	B	112 - 135	101 - 124
11	11	chain 'B' and (resid 146 through 171 )	B	B	146 - 171	126 - 151
12	12	chain 'B' and (resid 172 through 244 )	B	B	172 - 244	152 - 224
13	13	chain 'B' and (resid 245 through 322 )	B	B	245 - 322	225 - 302
14	14	chain 'B' and (resid 323 through 344 )	B	B	323 - 344	303 - 324

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