PDB-8wwq: geniposidic acid O-methyltransferase complexed with SAH and genip...

ID or keywords:

Entry

Database: PDB / ID: 8wwq

Title

geniposidic acid O-methyltransferase complexed with SAH and geniposidic acid

Components

geniposidic acid O-methyltransferase

Keywords

PLANT PROTEIN / Complex

Function / homology

S-ADENOSYL-L-HOMOCYSTEINE / :

Function and homology information

Biological species

Gardenia jasminoides (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.958 Å

Authors

Luo, Z. / Li, L. / Ma, D. / Zhou, H.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Structural insights into the substrate specificity of GAMT and divergence of seco-iridoid and closed-ring iridoid
Authors: Li, L. / Luo, Z. / Wei, W. / Zhan, R. / Zhou, H. / Ma, D.

History

Deposition	Oct 26, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 30, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8wwq.cif.gz	353.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8wwq.ent.gz	219 KB	Display	PDB format
PDBx/mmJSON format	8wwq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ww/8wwq ftp://data.pdbj.org/pub/pdb/validation_reports/ww/8wwq	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: geniposidic acid O-methyltransferase

B: geniposidic acid O-methyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	46.825, 103.086, 84.203
Angle α, β, γ (deg.)	90.000, 103.283, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	geniposidic acid O-methyltransferase Mass: 41581.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The sequence is available at GenBank with accession number PP815721.1 Source: (gene. exp.) Gardenia jasminoides (plant) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 261 molecules

#2: Chemical	ChemComp-XQ8 / Geniposidic acid Mass: 374.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₂₂O₁₀ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.38 Å³/Da / Density % sol: 48.28 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 0.1M BIS-TRIS pH6.0, 36% v/v Polypropylene glycol PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97903 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97903 Å / Relative weight: 1
Reflection	Resolution: 1.958→64.3 Å / Num. obs: 50211 / % possible obs: 89.8 % / Redundancy: 2.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.071 / Net I/σ(I): 7
Reflection shell	Resolution: 1.958→2.06 Å / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6731 / CC_1/2: 0.637

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
autoPROC		data reduction
autoPROC		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.958→64.232 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.934 / WR_factor R_free: 0.25 / WR_factor R_work: 0.206 / SU B: 8.763 / SU ML: 0.13 / Average fsc free: 0.9647 / Average fsc work: 0.9745 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.17
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2336	2385	4.966 %
R_work	0.1999	45642	-
all	0.202	-	-
obs	-	48027	85.825 %

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: 29.544 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.246 Å²	0 Å²	0.588 Å²
2-	-	-2.548 Å²	-0 Å²
3-	-	-	0.022 Å²

Refinement step

Cycle: LAST / Resolution: 1.958→64.232 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5137	0	88	254	5479

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	5355
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4889
X-RAY DIFFRACTION	r_angle_refined_deg	1.077	1.642	7271
X-RAY DIFFRACTION	r_angle_other_deg	0.395	1.58	11214
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.05	5	657
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.035	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.708	10	757
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.474	10	240
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	809
X-RAY DIFFRACTION	r_chiral_restr_other	0.055	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6362
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1278
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1060
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	4531
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	2667
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	2732
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	244
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.198	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.251	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.131	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.631	0.905	2653
X-RAY DIFFRACTION	r_mcbond_other	0.631	0.905	2653
X-RAY DIFFRACTION	r_mcangle_it	1.093	1.615	3301
X-RAY DIFFRACTION	r_mcangle_other	1.093	1.616	3302
X-RAY DIFFRACTION	r_scbond_it	0.752	1.008	2702
X-RAY DIFFRACTION	r_scbond_other	0.752	1.009	2703
X-RAY DIFFRACTION	r_scangle_it	1.266	1.817	3970
X-RAY DIFFRACTION	r_scangle_other	1.265	1.818	3971
X-RAY DIFFRACTION	r_lrange_it	4.169	9.487	5858
X-RAY DIFFRACTION	r_lrange_other	4.168	9.491	5859

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
1.958-2.009	0.292	188	0.263	3680	0.265	4086	0.951	0.963	94.6647	0.234
2.009-2.064	0.263	127	0.252	2518	0.252	4024	0.96	0.965	65.7306	0.225
2.064-2.124	0.249	131	0.243	2182	0.243	3928	0.966	0.967	58.8849	0.214
2.124-2.189	0.276	171	0.229	3449	0.231	3756	0.96	0.971	96.3791	0.201
2.189-2.261	0.27	131	0.232	2260	0.235	3705	0.96	0.971	64.5344	0.207
2.261-2.34	0.246	164	0.214	3062	0.215	3595	0.964	0.974	89.7357	0.191
2.34-2.428	0.251	171	0.214	3051	0.215	3377	0.961	0.973	95.4101	0.197
2.428-2.527	0.244	167	0.203	3007	0.206	3323	0.965	0.977	95.5161	0.189
2.527-2.639	0.225	149	0.198	2917	0.199	3202	0.968	0.978	95.7527	0.187
2.639-2.768	0.252	142	0.203	2752	0.205	3036	0.962	0.977	95.3228	0.197
2.768-2.917	0.238	107	0.197	2654	0.199	2890	0.967	0.978	95.5363	0.196
2.917-3.094	0.223	117	0.204	2428	0.204	2730	0.969	0.976	93.2234	0.209
3.094-3.307	0.261	96	0.2	2279	0.202	2550	0.965	0.978	93.1373	0.207
3.307-3.571	0.28	83	0.203	1579	0.207	2413	0.96	0.977	68.8769	0.218
3.571-3.911	0.218	83	0.194	1742	0.195	2222	0.973	0.98	82.1332	0.213
3.911-4.37	0.214	85	0.159	1721	0.161	1989	0.977	0.986	90.7994	0.186
4.37-5.042	0.192	109	0.146	1513	0.149	1766	0.983	0.988	91.846	0.18
5.042-6.166	0.256	66	0.202	1315	0.204	1505	0.968	0.979	91.7608	0.238
6.166-8.68	0.248	58	0.21	1009	0.212	1182	0.961	0.976	90.2707	0.261
8.68-64.232	0.106	38	0.191	514	0.185	667	0.992	0.975	82.7586	0.259

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	0.8647	-0.4754	-0.6151	1.0651	-0.272	0.9131	0.0646	0.0051	0.0987	-0.0036	0.0028	-0.0964	-0.0625	0.033	-0.0674	0.0692	-0.0186	-0.019	0.4709	0.0056	0.1115	15.561	8.708	2.298
2	0.2398	-0.0928	-0.1877	0.3865	0.05	0.1675	0.0181	-0.0064	0.001	0.0313	0.0061	-0.0267	-0.0383	-0.0328	-0.0242	0.0941	-0.0014	0.0052	0.4437	0.0116	0.1474	9.261	7.13	7.364
3	0.1526	-0.711	-0.3294	18.9914	4.912	13.4113	0.0082	0.2145	-0.1615	0.7241	0.1734	0.2791	0.5815	-1.2237	-0.1816	0.0982	-0.0171	-0.0819	0.5611	-0.124	0.3282	3.504	-18.858	-16.612
4	0.3976	-0.0376	0.0632	0.3208	0.1639	0.1207	0.0092	0.0972	-0.0383	-0.04	-0.025	0.0064	0.0049	-0.0588	0.0158	0.0979	-0.0023	0.0036	0.4707	0.0036	0.1165	12.247	-7.598	-12.508
5	3.0241	-0.304	-1.1455	0.9126	0.2156	0.4507	-0.0217	0.0116	0.1459	-0.2015	0.0779	-0.0154	-0.0292	-0.0353	-0.0562	0.1095	0.0296	-0.0008	0.4625	0.0558	0.1173	9.44	9.996	-11.257
6	2.5039	1.7598	-3.2759	6.7482	-1.025	5.1298	0.2089	-0.2282	0.3628	-0.0356	-0.0273	-0.2669	0.1327	0.1951	-0.1815	0.4298	-0.0684	0.3553	0.4814	-0.0886	0.4755	32.874	-2.024	-6.824
7	1.7359	-0.7596	-0.2114	0.5814	0.7986	2.0412	0.0425	-0.31	0.1073	0.0737	0.0917	-0.0979	0.2884	-0.0948	-0.1341	0.1389	-0.003	0.0026	0.4324	0.0204	0.1311	23.314	-15.895	-3.23
8	2.1873	-2.392	-0.1612	2.6414	0.0874	0.6634	0.0993	0.0956	0.1067	-0.1402	-0.1053	-0.1339	-0.033	0.0512	0.006	0.0959	-0.0026	0.0311	0.4168	0.0414	0.1691	26.29	0.226	-13.898
9	10.1586	-1.5123	3.6657	4.7603	-5.5084	6.7539	0.378	-0.6914	-0.8063	0.452	0.2584	0.4322	-0.4219	-0.4288	-0.6365	0.1364	0.1969	-0.0457	0.7008	-0.08	0.1781	-1.883	16.178	-5.193
10	12.5528	-14.9168	6.7861	18.1738	-7.8398	3.8139	-0.0297	-0.4948	-0.0952	0.0796	0.246	-0.251	0.1189	-0.488	-0.2163	0.4007	-0.1477	0.0057	0.7224	0.1209	0.3557	-7.004	-9.735	32.526
11	2.3442	-1.3098	0.5367	0.7601	-0.4467	1.3785	0.0593	-0.1227	-0.1721	-0.0469	0.0247	0.0823	-0.0181	-0.0986	-0.0841	0.0853	-0.0097	0.018	0.439	0.0182	0.1448	-11.775	3.105	22.785
12	0.6948	0.0271	-0.4718	0.0265	-0.1114	0.755	-0.0062	-0.0176	-0.0475	0.0122	-0.038	0.0193	-0.0162	0.0997	0.0442	0.0909	-0.016	0.0075	0.4829	0.007	0.1348	1.15	1.75	22.718
13	1.263	2.1767	-0.8505	8.6088	0.5574	6.6598	-0.4003	-0.1683	-0.292	-0.0223	-0.0991	-0.4417	-0.1101	1.1966	0.4993	0.3054	-0.0636	0.0346	0.7916	0.1017	0.1302	18.853	1.072	52.944
14	1.3596	-0.8642	0.8302	0.7941	-1.1303	2.3159	-0.0045	-0.0483	-0.0801	0.1576	0.0156	0.0968	-0.3651	0.2572	-0.0111	0.1687	-0.0438	0.0324	0.48	0.0198	0.114	4.145	7.355	40.216
15	0.0807	0.1474	-0.4183	0.2927	-0.8112	2.3208	-0.0476	-0.0479	-0.0396	-0.0301	-0.1339	-0.0433	0.0924	0.2531	0.1815	0.1456	-0.0016	0.0622	0.5643	0.0128	0.1069	6.359	-4.253	47.505
16	0.4388	-0.4138	0.8729	0.9569	-1.6046	2.9232	-0.0367	0.2119	-0.0962	-0.32	0.1104	0.0655	0.5054	0.1137	-0.0736	0.3053	-0.0949	0.0848	0.561	-0.028	0.1009	1.452	-7.781	39.161
17	21.5418	5.297	7.6705	1.3425	1.9079	2.7787	0.279	0.5824	-0.3613	0.0455	-0.0149	-0.1304	0.1225	0.2178	-0.2641	0.5792	0.4957	0.2359	1.0741	0.0362	0.6135	15.383	-18.96	43.982
18	0.8782	-1.7875	0.457	5.5272	-3.3271	3.3135	-0.0022	-0.0564	-0.0221	-0.2869	-0.0281	0.0468	0.3778	0.0808	0.0302	0.1332	-0.0321	0.0441	0.533	-0.0178	0.0892	-4.973	-5.413	43.637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	17 - 62
2	X-RAY DIFFRACTION	2	A	63 - 163
3	X-RAY DIFFRACTION	3	A	164 - 171
4	X-RAY DIFFRACTION	4	A	172 - 274
5	X-RAY DIFFRACTION	5	A	275 - 297
6	X-RAY DIFFRACTION	6	A	298 - 307
7	X-RAY DIFFRACTION	7	A	308 - 339
8	X-RAY DIFFRACTION	8	A	340 - 359
9	X-RAY DIFFRACTION	9	A	360 - 365
10	X-RAY DIFFRACTION	10	B	32 - 43
11	X-RAY DIFFRACTION	11	B	44 - 95
12	X-RAY DIFFRACTION	12	B	96 - 164
13	X-RAY DIFFRACTION	13	B	165 - 178
14	X-RAY DIFFRACTION	14	B	179 - 218
15	X-RAY DIFFRACTION	15	B	219 - 281
16	X-RAY DIFFRACTION	16	B	282 - 319
17	X-RAY DIFFRACTION	17	B	320 - 339
18	X-RAY DIFFRACTION	18	B	340 - 365

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