PDB-8gr7: Cop4 from Antrodia cinnamomea in complex with pyrophosphate and m...

ID or keywords:

Entry

Database: PDB / ID: 8gr7

Title

Cop4 from Antrodia cinnamomea in complex with pyrophosphate and magnesium

Components

AcCop4

Keywords

LYASE / Terpenoid / cubebol

Function / homology

DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE

Function and homology information

Biological species

Antrodia cinnamomea (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Chen, S.C. / Hsu, C.H.

Funding support

Taiwan, 1items

Citation

Journal: J.Agric.Food Chem. / Year: 2023
Title: Characterization and Crystal Structures of a Cubebol-Producing Sesquiterpene Synthase from Antrodia cinnamomea .
Authors: Chen, S.C. / Jiang, B.C. / Lu, Y.J. / Chang, C.H. / Wu, T.H. / Lin, S.W. / Yin, H.W. / Lee, T.H. / Hsu, C.H.

History

Deposition	Sep 1, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gr7.cif.gz	280.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8gr7.ent.gz	224.8 KB	Display	PDB format
PDBx/mmJSON format	8gr7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gr7_validation.pdf.gz	5.1 MB	Display	wwPDB validaton report
Full document	8gr7_full_validation.pdf.gz	5.1 MB	Display
Data in XML	8gr7_validation.xml.gz	29.2 KB	Display
Data in CIF	8gr7_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/8gr7 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/8gr7	HTTPS FTP

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Related structure data

Related structure data	8gr5SC S: Starting model for refinement C: citing same article (ref.)
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: AcCop4

B: AcCop4

hetero molecules

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

1

A: AcCop4

hetero molecules

defined by author
Evidence: gel filtration, monomer
39.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: AcCop4

hetero molecules

defined by author
39.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.203, 45.224, 79.324
Angle α, β, γ (deg.)	85.060, 78.050, 79.950
Int Tables number	1
Space group name H-M	P1
Symmetry operation	#1: x,y,z

#1: Protein	AcCop4 Mass: 39362.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Antrodia cinnamomea (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PPV / PYROPHOSPHATE Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₄O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H₂O
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: 2.03 Å³/Da / Density % sol: 39.48 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: HEPES pH 7.5, 10% 2-Propanol, 20% PEG 4000

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Data collection

Diffraction	Mean temperature: 173 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 9, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. obs: 46461 / % possible obs: 97.6 % / Redundancy: 4 % / B_iso Wilson estimate: 19.03 Å² / R_pim(I) all: 0.04 / Net I/σ(I): 17.8
Reflection shell	Resolution: 1.9→1.97 Å / Num. unique obs: 4628 / CC_1/2: 0.891

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8GR5

8gr5

Resolution: 1.9→27.98 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2061	1999	4.75 %
R_work	0.1623	40066	-
obs	0.1644	42065	88.33 %

Solvent computation

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

Displacement parameters

B_iso max: 78.36 Å² / B_iso mean: 23.0633 Å² / B_iso min: 4.75 Å²

Refinement step

Cycle: final / Resolution: 1.9→27.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5233	0	54	489	5776
B_iso mean	-	-	38.63	33.57	-
Num. residues	-	-	-	-	651

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.95	0.2639	70	0.1917	1403	1473	43
1.95-2	0.2393	92	0.1803	1860	1952	57
2-2.06	0.2308	121	0.1809	2412	2533	74
2.06-2.13	0.2336	136	0.1723	2705	2841	85
2.13-2.2	0.1962	152	0.1678	3051	3203	95
2.2-2.29	0.2246	158	0.1573	3165	3323	97
2.29-2.39	0.1933	158	0.1512	3187	3345	98
2.39-2.52	0.2186	158	0.1595	3157	3315	98
2.52-2.68	0.2226	158	0.1693	3178	3336	98
2.68-2.88	0.2408	157	0.1612	3138	3295	98
2.88-3.17	0.2042	161	0.1669	3208	3369	98
3.17-3.63	0.1915	158	0.1568	3191	3349	98
3.63-4.57	0.1793	161	0.1413	3202	3363	99
4.57-27.98	0.1974	159	0.1783	3209	3368	99

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	0.0059	0.0053	0.0022	0.0177	0.0038	0.0036	0.0258	0.0891	0.0392	-0.0964	0.0262	0.0428	0.0125	-0.0132	0.0002	0.1056	0.0202	-0.0075	0.13	0.0083	0.1073	11.4463	-22.9454	-31.0705
2	0.009	-0.0004	0.0105	0.0506	-0.0255	0.0382	0.018	0.0907	-0.0629	-0.0019	0.0411	0.0101	0.0368	-0.0235	0.0243	0.0757	0.0124	-0.013	0.0805	-0.0183	0.0843	16.742	-30.1016	-26.2467
3	0.4175	0.0351	0.0155	0.2995	0.0059	0.283	0.1527	-0.1334	-0.2971	0.0389	-0.0413	0.0075	0.0815	-0.1326	0.4848	0.0894	-0.0459	-0.0526	0.0199	0.0278	0.1027	10.1511	-34.5077	-15.7076
4	0.0777	0.0613	0.0782	0.1323	-0.0209	0.1046	0.053	-0.0393	-0.1085	0.1201	-0.0068	-0.0673	-0.0224	-0.02	0.0237	0.0869	-0.0151	-0.0304	0.1026	-0.0065	0.0962	17.9198	-26.3929	-9.234
5	0.0321	0.0111	0.0001	0.0008	-0.0008	0.0084	-0.0275	0.0829	-0.0297	-0.0704	0.0243	-0.0451	-0.0404	0.0438	0.0099	0.1682	-0.06	0.0526	0.1961	-0.0484	0.1104	29.3179	-19.3323	6.1462
6	0.0059	0.0015	0.0035	0.0047	0.0069	0.0071	0.0433	0.1366	0.1471	-0.0394	0.0153	0.0767	-0.0742	-0.1181	-0.0002	0.1081	0.0177	0.0212	0.1088	0.0298	0.2678	6.7053	-15.6963	15.9118
7	0.0273	0.0069	0.0055	0.0059	0.0113	0.0332	-0.0303	0.0684	0.0702	0.026	0.1095	0.0194	-0.0197	-0.0812	0	0.0789	0.0088	0.0112	0.1081	0.0051	0.0978	15.6147	-21.2572	18.5754
8	0.0192	-0.0042	0.0018	0.0021	0.0025	0.0093	0.0069	-0.0971	0.0089	0.0392	0.0242	0.0143	-0.0067	0.0713	0.0341	0.1725	0.0108	0.0804	0.143	-0.0043	0.1994	15.0429	-8.6493	33.212
9	0.1471	0.0609	0.0093	0.0264	0.0212	0.2022	0.088	0.0685	0.0452	0.0301	0.1033	0.0729	-0.0524	-0.0286	0.2251	0.0171	0.058	0.2711	0.1138	0.0154	0.1115	9.4226	-21.6984	32.61
10	0.0464	0.0146	0.0436	0.0216	0.0112	0.036	0.0224	-0.0793	0.0546	0.0716	-0.0034	-0.0066	0.005	0.0276	0.0119	0.1284	0.0197	0.0254	0.0984	-0.0111	0.0922	23.4485	-12.3899	31.5416
11	0.0441	-0.0051	0.0499	0.0186	0.007	0.0351	-0.0162	0.0051	-0.0333	0.0712	0.0788	-0.0037	-0.038	0.0179	0.0003	0.0852	0.0207	-0.0098	0.0913	-0.0197	0.0953	29.6321	-18.941	26.8277
12	0.0632	0.0263	0.1101	0.2949	0.1079	0.1324	-0.0531	0.0067	-0.0023	-0.0913	0.1337	-0.2172	-0.0704	0.0615	0.0357	0.0667	-0.0029	0.0225	0.0984	-0.0348	0.1014	35.2381	-13.3182	16.3548
13	0.083	-0.0106	-0.0879	0.0211	0.0242	0.1298	0.0439	0.0903	-0.1147	-0.0472	0.1096	-0.0596	0.0446	0.0494	0.0867	0.077	0.0169	-0.0287	0.079	-0.028	0.1115	28.7506	-28.0941	16.4246
14	0.0076	0.003	0.005	0.0059	-0.0007	0.0132	0.025	0.025	0.0548	-0.0352	0.0373	0.0914	-0.0696	-0.0167	-0	0.1854	-0.0259	-0.002	0.1603	-0.0045	0.113	22.5752	-8.7721	2.4405
15	0.0367	0.0137	-0.0047	0.0112	0.0116	0.0372	0.05	-0.027	-0.0369	0.0224	0.0364	0.0149	0.0645	-0.0738	0.0731	0.1438	-0.0786	-0.0247	0.131	0.129	-0.0412	17.1201	-29.5758	-5.7211
16	0.041	0.0314	-0.0305	0.0416	-0.0408	0.0691	0.0783	-0.0832	0.0993	0.1133	-0.0282	0.0621	-0.135	-0.0464	0.0071	0.0931	0.008	0.0085	0.0587	0.0025	0.0998	19.8106	-12.5222	-17.1764
17	0.003	0.0037	0.0053	0.0084	0.0008	0.0071	0.0182	0.0408	0.0056	-0.0324	0.0383	0.0557	0.0208	0.0007	0	0.1726	-0.0183	-0.0179	0.1991	0.0406	0.1423	9.2171	-13.8799	-32.8966
18	0.0392	0.0009	0.0053	0.0148	0.0071	0.0072	-0.0435	0.0405	0.1019	-0.0335	0.0224	0.0013	-0.0213	0.0997	0.0042	0.1176	-0.0058	-0.0276	0.146	0.1046	0.0907	22.9548	-10.7472	-32.427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 137 through 163 )	B	137 - 163
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 164 through 204 )	B	164 - 204
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 205 through 281 )	B	205 - 281
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 282 through 330 )	B	282 - 330
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 6 through 26 )	A	6 - 26
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 27 through 54 )	A	27 - 54
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 55 through 92 )	A	55 - 92
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 93 through 110 )	A	93 - 110
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 111 through 136 )	A	111 - 136
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 137 through 163 )	A	137 - 163
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 164 through 204 )	A	164 - 204
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 205 through 281 )	A	205 - 281
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 282 through 308 )	A	282 - 308
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 309 through 331 )	A	309 - 331
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 6 through 26 )	B	6 - 26
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 27 through 92 )	B	27 - 92
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 93 through 110 )	B	93 - 110
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 111 through 136 )	B	111 - 136

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