PDB-7waq: SbSOMT in complex with resveratrol

ID or keywords:

Entry

Database: PDB / ID: 7waq

Title

SbSOMT in complex with resveratrol

Components

stilbene O-methyltransferase

Keywords

TRANSFERASE / resveratrol / complex / o-methyltransferase / substrate

Function / homology

Function and homology information

S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity / nucleotide binding
Similarity search - Function

Biological species

Sorghum bicolor (sorghum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.56 Å

Authors

Pow, K.C. / Hao, Q.

Funding support

Hong Kong, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Regioselective stilbene O-methylations in Saccharinae grasses.
Authors: Lui, A.C.W. / Pow, K.C. / Lin, N. / Lam, L.P.Y. / Liu, G. / Godwin, I.D. / Fan, Z. / Khoo, C.J. / Tobimatsu, Y. / Wang, L. / Hao, Q. / Lo, C.

History

Deposition	Dec 14, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2023	Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2	Jun 21, 2023	Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7waq.cif.gz	744.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7waq.ent.gz	476.4 KB	Display	PDB format
PDBx/mmJSON format	7waq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7waq_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7waq_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7waq_validation.xml.gz	54.2 KB	Display
Data in CIF	7waq_validation.cif.gz	72.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wa/7waq ftp://data.pdbj.org/pub/pdb/validation_reports/wa/7waq	HTTPS FTP

-
Related structure data

Related structure data	7vb8SC 7warC 7wasC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#213 - Sep 2017 Sirtuins similarity (1)

Deposited unit

B: stilbene O-methyltransferase

A: stilbene O-methyltransferase

C: stilbene O-methyltransferase

D: stilbene O-methyltransferase

hetero molecules

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

1

D: stilbene O-methyltransferase

hetero molecules

B: stilbene O-methyltransferase

hetero molecules

defined by author&software
Evidence: homology
83.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: stilbene O-methyltransferase

C: stilbene O-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.485, 111.733, 131.102
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	B
3	2	B
4	2	B
5	3	B
6	3	B
7	4	B
8	4	B
9	5	B
10	5	B
11	6	B
12	6	B

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / Auth asym-ID: B / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	15 - 376	14 - 375
2	1	1	THR	THR	15 - 376	14 - 375
3	2	2	THR	THR	15 - 376	14 - 375
4	2	2	THR	THR	15 - 376	14 - 375
5	3	3	THR	THR	15 - 376	14 - 375
6	3	3	THR	THR	15 - 376	14 - 375
7	4	4	LYS	LYS	15 - 377	14 - 376
8	4	4	LYS	LYS	15 - 377	14 - 376
9	5	5	THR	THR	15 - 376	14 - 375
10	5	5	THR	THR	15 - 376	14 - 375
11	6	6	THR	THR	15 - 376	14 - 375
12	6	6	THR	THR	15 - 376	14 - 375

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	stilbene O-methyltransferase Mass: 41402.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_3007G059100 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: A0A1B6PFV1
#2: Chemical	ChemComp-STL / RESVERATROL Mass: 228.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₁₂O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.85 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulphate, 30% (w/v) polyethylene glycol monomethyl ether 5000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.55→48.956 Å / Num. obs: 46864 / % possible obs: 99.9 % / Redundancy: 13.2 % / B_iso Wilson estimate: 52.2 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.118 / R_pim(I) all: 0.048 / R_rim(I) all: 0.127 / Net I/σ(I): 16.3
Reflection shell	Resolution: 2.56→2.65 Å / Redundancy: 13.6 % / R_merge(I) obs: 1.156 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4537 / CC_1/2: 0.902 / R_pim(I) all: 0.468 / R_rim(I) all: 1.247 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7VB8

7vb8

Resolution: 2.56→48.956 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.933 / WR_factor R_free: 0.227 / WR_factor R_work: 0.164 / SU B: 30.481 / SU ML: 0.291 / Average fsc free: 0.9427 / Average fsc work: 0.9679 / Cross valid method: FREE R-VALUE / ESU R Free: 0.339
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2567	2368	5.06 %
R_work	0.1864	44434	-
all	0.19	-	-
obs	-	46802	99.932 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 65.847 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.587 Å²	-0 Å²	-0 Å²
2-	-	0.516 Å²	-0 Å²
3-	-	-	6.072 Å²

Refinement step

Cycle: LAST / Resolution: 2.56→48.956 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11270	0	92	63	11425

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.012	11615
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10764
X-RAY DIFFRACTION	r_angle_refined_deg	2.381	1.636	15736
X-RAY DIFFRACTION	r_angle_other_deg	0.79	1.549	24984
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.285	5	1456
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.694	10	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.332	10	1954
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.446	10	494
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	1786
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	13202
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2346
X-RAY DIFFRACTION	r_nbd_refined	0.238	0.2	2500
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	10113
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	5570
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	6470
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	201
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.142	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.182	0.2	37
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	256
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.119	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	7.051	4.078	5830
X-RAY DIFFRACTION	r_mcbond_other	7.05	4.078	5830
X-RAY DIFFRACTION	r_mcangle_it	9.851	6.084	7284
X-RAY DIFFRACTION	r_mcangle_other	9.851	6.084	7285
X-RAY DIFFRACTION	r_scbond_it	7.85	4.44	5785
X-RAY DIFFRACTION	r_scbond_other	7.849	4.44	5786
X-RAY DIFFRACTION	r_scangle_it	10.459	6.458	8452
X-RAY DIFFRACTION	r_scangle_other	10.458	6.457	8453
X-RAY DIFFRACTION	r_lrange_it	12.62	53.492	12715
X-RAY DIFFRACTION	r_lrange_other	12.62	53.489	12714
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.133	0.05	10696
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.135	0.05	10720
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.138	0.05	10653
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.138	0.05	10731
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.139	0.05	10639
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.13	0.05	10710

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.13343	0.05006
1	2	B	X-RAY DIFFRACTION	Local ncs	0.13343	0.05006
2	3	B	X-RAY DIFFRACTION	Local ncs	0.13525	0.05006
2	4	B	X-RAY DIFFRACTION	Local ncs	0.13525	0.05006
3	5	B	X-RAY DIFFRACTION	Local ncs	0.13803	0.05006
3	6	B	X-RAY DIFFRACTION	Local ncs	0.13803	0.05006
4	7	B	X-RAY DIFFRACTION	Local ncs	0.13767	0.05006
4	8	B	X-RAY DIFFRACTION	Local ncs	0.13767	0.05006
5	9	B	X-RAY DIFFRACTION	Local ncs	0.13877	0.05007
5	10	B	X-RAY DIFFRACTION	Local ncs	0.13877	0.05007
6	11	B	X-RAY DIFFRACTION	Local ncs	0.13017	0.05007
6	12	B	X-RAY DIFFRACTION	Local ncs	0.13017	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.56-2.626	0.35	187	0.302	3210	0.304	3398	0.897	0.927	99.9706	0.281
2.626-2.698	0.334	192	0.273	3129	0.276	3322	0.93	0.94	99.9699	0.247
2.698-2.776	0.318	162	0.273	3076	0.275	3238	0.918	0.943	100	0.249
2.776-2.861	0.326	143	0.239	3010	0.243	3157	0.927	0.959	99.8733	0.213
2.861-2.955	0.289	164	0.222	2889	0.226	3056	0.942	0.969	99.9018	0.195
2.955-3.058	0.321	137	0.218	2791	0.222	2930	0.92	0.969	99.9317	0.189
3.058-3.173	0.331	152	0.219	2715	0.225	2868	0.93	0.967	99.9651	0.192
3.173-3.302	0.308	129	0.22	2624	0.225	2753	0.927	0.968	100	0.193
3.302-3.448	0.278	129	0.204	2503	0.208	2632	0.948	0.973	100	0.182
3.448-3.616	0.303	121	0.178	2428	0.183	2553	0.942	0.981	99.8433	0.16
3.616-3.81	0.224	116	0.166	2284	0.168	2402	0.968	0.983	99.9167	0.148
3.81-4.04	0.237	103	0.161	2175	0.165	2278	0.967	0.984	100	0.146
4.04-4.316	0.213	133	0.15	2034	0.154	2167	0.97	0.986	100	0.137
4.316-4.659	0.221	101	0.146	1924	0.15	2025	0.98	0.988	100	0.136
4.659-5.099	0.21	104	0.139	1765	0.143	1869	0.978	0.99	100	0.132
5.099-5.693	0.258	81	0.175	1602	0.179	1683	0.971	0.984	100	0.164
5.693-6.559	0.317	65	0.184	1456	0.189	1521	0.94	0.978	100	0.172
6.559-7.998	0.185	73	0.148	1218	0.151	1291	0.977	0.986	100	0.146
7.998-11.163	0.169	47	0.13	993	0.132	1041	0.983	0.991	99.9039	0.135
11.163-48.956	0.231	29	0.234	608	0.234	641	0.969	0.974	99.376	0.25

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	1.9872	-0.3594	0.5279	1.305	-0.3759	1.3411	0.0049	-0.2029	-0.0296	0.1139	0.0671	0.0729	0.0046	-0.1518	-0.072	0.1942	-0.0296	0.048	0.0413	0.004	0.0171	-31.3589	5.5848	-26.5624
2	1.7248	0.279	-0.0025	1.4081	0.2668	0.9357	-0.0497	0.5647	-0.1373	-0.2761	-0.0298	0.1484	-0.0004	-0.1691	0.0795	0.2991	0.0175	0.0328	0.4026	-0.059	0.117	-66.1502	2.6832	-3.0117
3	2.4216	-0.0656	0.2388	1.4072	0.0146	1.2071	-0.0555	-0.0834	0.2548	0.0952	-0.0508	0.0321	-0.1254	-0.0541	0.1063	0.2198	0.0383	0.0216	0.0838	0.0013	0.0399	-54.004	19.4074	21.3038
4	2.2204	0.335	0.3682	1.0875	0.4135	1.3835	0.0072	-0.3209	0.4042	0.0674	0.0586	-0.0703	-0.1436	0.106	-0.0658	0.2386	0.0056	0.0421	0.1669	-0.1012	0.1087	-53.8189	-33.6437	-14.7796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	B	15 - 377
2	X-RAY DIFFRACTION	1		B	401 - 402
3	X-RAY DIFFRACTION	2		A	14 - 377
4	X-RAY DIFFRACTION	2		A	401 - 402
5	X-RAY DIFFRACTION	3		C	14 - 377
6	X-RAY DIFFRACTION	3		C	401 - 402
7	X-RAY DIFFRACTION	4		D	13 - 377
8	X-RAY DIFFRACTION	4		D	401 - 403

-
News

-
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.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi