PDB-4ems: Crystal Structure Analysis of Coniferyl Alcohol 9-O-Methyltransfe...

ID or keywords:

Entry

Database: PDB / ID: 4ems

Title

Crystal Structure Analysis of Coniferyl Alcohol 9-O-Methyltransferase from Linum Nodiflorum

Components

Coniferyl alcohol 9-O-methyltransferase

Keywords

TRANSFERASE / Rossmann fold / Dimer / small molecule O-methyltransferase / S-Adenosyl-L-methionine / coniferyl alcohol / phenylpropanoid / methylation

Function / homology

Function and homology information

acetylserotonin O-methyltransferase activity / melatonin biosynthetic process / methylation / protein dimerization activity
Similarity search - Function

Biological species

Linum nodiflorum (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD,

MOLECULAR REPLACEMENT /

SAD /

molecular replacement / Resolution: 1.7534 Å

Authors

Wolters, S. / Heine, A. / Petersen, M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural analysis of coniferyl alcohol 9-O-methyltransferase from Linum nodiflorum reveals a novel active-site environment.
Authors: Wolters, S. / Neeb, M. / Berim, A. / Schulze Wischeler, J. / Petersen, M. / Heine, A.

History

Deposition	Apr 12, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ems.cif.gz	306 KB	Display	PDBx/mmCIF format
PDB format	pdb4ems.ent.gz	246.9 KB	Display	PDB format
PDBx/mmJSON format	4ems.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ems_validation.pdf.gz	454.5 KB	Display	wwPDB validaton report
Full document	4ems_full_validation.pdf.gz	460.1 KB	Display
Data in XML	4ems_validation.xml.gz	33 KB	Display
Data in CIF	4ems_validation.cif.gz	49.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/4ems ftp://data.pdbj.org/pub/pdb/validation_reports/em/4ems	HTTPS FTP

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Related structure data

Related structure data	4e70C 4eviC C: citing same article (ref.)
Similar structure data	4evi-d 6tz6-1 6i6n-d 4zg9-1 3tky-1 4e70-d 5cvj-1 6neg-d 6i73-d 3tky-2 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: Coniferyl alcohol 9-O-methyltransferase

B: Coniferyl alcohol 9-O-methyltransferase

hetero molecules

87.3 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)	76.149, 104.562, 109.875
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Coniferyl alcohol 9-O-methyltransferase / S-adenosyl-L-methionine-dependent coniferyl alcohol 9-O-methyltransferase Mass: 43425.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Linum nodiflorum (plant) / Gene: CA9OMT / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A6XNE6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1 M Na/K phosphate, 0,7M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.91841 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009 / Details: Mirror, Double Crystal Monochromator

Radiation

Monochromator: Double Crystal Monochromator Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91841 Å / Relative weight: 1

Reflection

Redundancy: 4.9 % / Av σ(I) over netI: 20.86 / Number: 193474 / R_merge(I) obs: 0.109 / Χ²: 3.93 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 39655 / % possible obs: 98.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.24	50	97.7	1	0.083	16.344	4.4
4.95	6.24	99.4	1	0.089	9.488	4.8
4.33	4.95	99.1	1	0.077	8.286	4.7
3.93	4.33	99.5	1	0.08	6.339	4.9
3.65	3.93	99.4	1	0.084	5.317	5
3.44	3.65	99.3	1	0.091	4.606	5.1
3.26	3.44	99.2	1	0.101	3.786	5.1
3.12	3.26	99.5	1	0.119	3.181	5.1
3	3.12	99.8	1	0.148	2.84	5.1
2.9	3	99.8	1	0.165	2.412	5.1
2.81	2.9	99.6	1	0.191	2.156	5
2.73	2.81	99.7	1	0.221	1.871	5
2.66	2.73	99.6	1	0.24	1.805	4.9
2.59	2.66	99.5	1	0.276	1.683	4.9
2.53	2.59	98.9	1	0.296	1.531	4.9
2.48	2.53	98.6	1	0.347	1.509	4.8
2.43	2.48	97.7	1	0.379	1.354	4.8
2.38	2.43	97.6	1	0.429	1.375	4.8
2.34	2.38	97.1	1	0.458	1.259	4.8
2.3	2.34	96.3	1	0.459	1.177	4.3

Reflection

Resolution: 1.75→30 Å / Num. all: 87649 / Num. obs: 87649 / % possible obs: 99.2 % / Redundancy: 4.4 % / R_sym value: 0.061 / Χ²: 1.01 / Net I/σ(I): 14.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.75-1.78	4.5	0.45	4364	0.955	1	99.9
1.78-1.81	4.5	0.403	4366	0.96	1	99.8
1.81-1.85	4.5	0.34	4355	0.935	1	99.7
1.85-1.89	4.5	0.284	4340	0.978	1	99.8
1.89-1.93	4.4	0.258	4358	1.118	1	99.6
1.93-1.97	4.5	0.198	4360	0.965	1	99.9
1.97-2.02	4.5	0.159	4375	0.95	1	99.9
2.02-2.07	4.4	0.133	4362	1.032	1	99.7
2.07-2.14	4.5	0.109	4375	0.944	1	99.9
2.14-2.2	4.5	0.089	4367	0.973	1	99.9
2.2-2.28	4.4	0.093	4382	1.009	1	99.5
2.28-2.37	4.5	0.076	4404	1.034	1	99.8
2.37-2.48	4.5	0.077	4401	1.101	1	99.8
2.48-2.61	4.4	0.078	4408	1.087	1	99.6
2.61-2.78	4.4	0.081	4379	1.069	1	99.5
2.78-2.99	4.5	0.076	4385	1.078	1	99.3
2.99-3.29	4.5	0.064	4436	1.047	1	98.9
3.29-3.77	4.5	0.042	4412	1.056	1	98.7
3.77-4.74	4.4	0.024	4429	0.983	1	97.7
4.74-30	4.2	0.02	4391	0.928	1	93.2

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Phasing

Phasing

Method
SAD
molecular replacement

Phasing MR

R_factor: 27.18 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	30 Å
Translation	2.5 Å	30 Å

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 89365

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.42-100	25.9	0.808	2190
3.83-5.42	20.3	0.89	4614
3.13-3.83	18.9	0.886	6319
2.71-3.13	19.5	0.88	7538
2.42-2.71	19.6	0.891	8665
2.21-2.42	18	0.898	9638
2.05-2.21	18.2	0.898	10562
1.92-2.05	19	0.894	11424
1.81-1.92	20	0.885	12174
1.71-1.81	22.4	0.873	12979
1-1.71	28.5	0.827	3262

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER	2.1.4	phasing
SHELX		phasing
DM	6.1	phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
MAR345dtb		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

SAD,

MOLECULAR REPLACEMENT / Resolution: 1.7534→29.997 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.89 / SU ML: 0.45 / σ(F): 1.34 / Phase error: 17.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19	4391	5.02 %	Random
R_work	0.1636	-	-	-
obs	0.1649	87549	98.94 %	-
all	-	87649	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.201 Å² / k_sol: 0.378 e/Å³

Displacement parameters

B_iso max: 79.03 Å² / B_iso mean: 22.6705 Å² / B_iso min: 7.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.6581 Å²	0 Å²	0 Å²
2-	-	1.0759 Å²	0 Å²
3-	-	-	1.5822 Å²

Refinement step

Cycle: LAST / Resolution: 1.7534→29.997 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5518	0	30	629	6177

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5873
X-RAY DIFFRACTION	f_angle_d	1.017	8020
X-RAY DIFFRACTION	f_chiral_restr	0.071	898
X-RAY DIFFRACTION	f_plane_restr	0.005	1032
X-RAY DIFFRACTION	f_dihedral_angle_d	12.187	2090

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7534-1.7733	0.2404	136	0.2145	2615	2751	93
1.7733-1.7942	0.2578	138	0.2156	2742	2880	100
1.7942-1.816	0.2657	127	0.2109	2794	2921	100
1.816-1.839	0.2498	134	0.1982	2753	2887	100
1.839-1.8632	0.2366	160	0.1962	2782	2942	100
1.8632-1.8887	0.2551	154	0.1766	2747	2901	100
1.8887-1.9157	0.2089	144	0.184	2732	2876	99
1.9157-1.9443	0.2272	157	0.1689	2757	2914	100
1.9443-1.9747	0.2011	161	0.1627	2751	2912	100
1.9747-2.0071	0.2068	147	0.1654	2778	2925	100
2.0071-2.0417	0.1858	149	0.1634	2763	2912	100
2.0417-2.0788	0.1798	135	0.1615	2778	2913	100
2.0788-2.1188	0.1855	144	0.1605	2780	2924	100
2.1188-2.162	0.1884	152	0.1546	2783	2935	100
2.162-2.209	0.185	137	0.1528	2766	2903	100
2.209-2.2604	0.1961	142	0.1618	2792	2934	99
2.2604-2.3169	0.1714	149	0.1545	2789	2938	100
2.3169-2.3795	0.1843	146	0.1521	2780	2926	100
2.3795-2.4495	0.1705	136	0.1581	2785	2921	100
2.4495-2.5285	0.193	148	0.1617	2806	2954	100
2.5285-2.6188	0.2066	138	0.1634	2809	2947	100
2.6188-2.7236	0.2133	150	0.1716	2761	2911	99
2.7236-2.8475	0.2114	151	0.1827	2772	2923	100
2.8475-2.9975	0.197	148	0.1696	2799	2947	99
2.9975-3.1851	0.1874	150	0.166	2816	2966	99
3.1851-3.4307	0.1795	160	0.1637	2782	2942	99
3.4307-3.7753	0.1723	160	0.1468	2784	2944	98
3.7753-4.3202	0.1496	145	0.1398	2801	2946	98
4.3202-5.4377	0.1537	140	0.1392	2829	2969	97
5.4377-30.0011	0.2075	153	0.1937	2732	2885	91

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	8.7533	2.3987	-1.9894	1.3832	-0.4664	1.5284	0.2013	-0.1801	0.1203	-0.0266	-0.0757	-0.0859	-0.1268	0.1694	-0.117	0.1617	0.0019	0.0084	0.0782	-0.0162	0.0649	-0.8272	-14.8036	22.1893
2	1.8693	0.3345	0.3125	2.4687	-0.5177	2.3326	-0.0612	0.1114	-0.1443	-0.3873	0.0578	0.1067	0.1005	-0.0293	-0.0188	0.1433	-0.0107	-0.0342	0.064	-0.0266	0.0434	-15.4126	-32.218	17.8419
3	1.6766	0.7937	-0.0981	2.1396	-1.9319	2.1964	0.0369	-0.0773	0.0726	0.2817	0.0663	0.4226	0.0654	-0.0987	-0.1025	0.1322	0.0099	-0.0199	0.2057	-0.0242	0.1479	-19.2992	-25.5938	34.4613
4	4.2745	0.3412	-1.0448	3.0214	-0.3239	2.1391	0.0421	-0.2708	0.1451	-0.0005	-0.0802	0.5589	-0.2063	-0.2518	0.0895	0.1721	0.0679	-0.0026	0.158	-0.0375	0.191	-16.0127	-2.6301	40.8451
5	2.1009	0.073	-0.7533	1.6294	-0.0244	1.9564	-0.0076	0.0523	-0.1641	-0.0446	0.0538	0.2264	-0.002	-0.164	-0.0242	0.0377	-0.014	0.0095	0.1043	-0.0061	0.149	-16.8848	-30.1559	51.1967
6	3.6215	-0.218	0.0816	1.8852	-0.2092	1.0889	-0.0258	-0.1791	0.0443	0.3166	0.0467	0.2033	-0.1143	-0.0258	-0.0061	0.0676	-0.001	0.0629	0.1425	0.0178	0.1585	-23.7649	-25.6482	59.2909
7	2.1038	-0.4044	-0.1771	2.1607	-0.0355	1.3345	0.0943	-0.1931	0.0685	0.1696	-0.0144	0.0892	-0.1093	-0.0655	-0.0833	0.0714	-0.0183	0.003	0.1381	0.0033	0.084	-7.9416	-20.1011	57.2065
8	1.439	0.306	0.7561	1.8314	-0.9595	3.5065	-0.0184	-0.1434	0.0738	0.0248	0.0465	0.0135	-0.176	-0.0322	-0.0222	0.0591	-0.0108	0.0147	0.0757	-0.0061	0.0703	-3.4585	-15.2344	48.19
9	1.6134	0.397	0.6155	2.9688	2.131	6.3707	0.0975	-0.2046	-0.0703	0.2409	0.0308	-0.0906	0.3147	0.159	-0.1441	0.0635	-0.0102	-0.0042	0.1393	0.0256	0.0888	-2.6815	-26.5999	58.1109
10	0.6567	0.8648	-0.4625	7.084	-3.1611	2.2506	-0.0862	0.0344	-0.0543	-0.3442	0.1976	0.081	0.1021	-0.1025	-0.1057	0.0813	0.0009	-0.0113	0.1091	-0.0207	0.0608	-7.2514	-21.375	35.5214
11	2.894	0.6919	-0.6129	2.3489	0.1214	1.7299	-0.0323	-0.0732	0.2344	0.0572	0.0175	-0.0455	-0.2144	0.0549	0.0048	0.1332	-0.0193	-0.0202	0.0581	-0.015	0.075	5.063	-1.0176	40.3867
12	2.6149	0.9382	0.9863	1.3221	0.4374	0.6153	-0.0494	-0.0844	0.0993	-0.1026	0.0347	-0.0577	-0.1513	-0.0374	0.0314	0.1611	0.0043	0.0325	0.1092	-0.0292	0.0863	0.5314	-6.4938	28.2663
13	3.6078	1.7058	0.2465	4.57	-1.2062	2.0605	-0.2108	0.1887	0.4919	-0.8098	0.1438	0.4404	-0.1605	-0.049	0.0915	0.3408	0.0456	-0.0838	0.1711	0.0341	0.1953	-19.3154	-6.7629	11.2823
14	1.6845	-0.4106	-0.9352	0.8502	0.3295	3.0301	0.0222	0.0381	0.1321	-0.0571	0.0459	-0.0413	-0.2422	0.1115	-0.0847	0.2211	-0.0593	0.045	0.1332	-0.0199	0.1828	7.8776	-4.9656	6.5338
15	2.8904	-0.3743	2.4085	5.5706	0.5484	4.0312	-0.1032	-0.0052	0.617	-0.1394	-0.0315	0.3127	-0.2223	-0.0835	0.0928	0.1903	-0.04	0.0515	0.1312	-0.0088	0.1962	9.9659	1.5252	0.2329
16	2.606	0.4489	-0.393	1.8418	-0.1452	2.3755	-0.0006	0.4067	0.2235	-0.268	0.1274	0.0551	-0.1239	-0.1529	-0.1062	0.2006	-0.0044	0.0476	0.1832	0.0037	0.1238	0.6187	-13.4804	-1.3416
17	1.9036	0.1858	-1.6297	0.4061	0.2833	2.3647	0.0273	0.2269	-0.0399	-0.1407	-0.0008	-0.0543	0.0822	-0.0675	-0.0314	0.1593	-0.0095	0.0282	0.096	-0.0122	0.0692	0.5966	-19.7311	5.5911

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:34)	A	1 - 34
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 35:106)	A	35 - 106
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 107:124)	A	107 - 124
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 125:168)	A	125 - 168
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 169:221)	A	169 - 221
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 222:262)	A	222 - 262
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 263:312)	A	263 - 312
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 313:347)	A	313 - 347
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 348:368)	A	348 - 368
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 0:34)	B	0 - 34
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 35:77)	B	35 - 77
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 78:138)	B	78 - 138
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 139:168)	B	139 - 168
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 169:212)	B	169 - 212
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 213:250)	B	213 - 250
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 251:312)	B	251 - 312
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 313:368)	B	313 - 368

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
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