PDB-5bu3: Crystal Structure of Diels-Alderase PyrI4 in complex with its product

ID or keywords:

Entry

Database: PDB / ID: 5bu3

Title

Crystal Structure of Diels-Alderase PyrI4 in complex with its product

Components

PyrI4

Keywords

LYASE / Diels-Alderase / Complex

Function / homology

Allene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / Isomerases / antibiotic biosynthetic process / isomerase activity / Chem-4W9 / Spiro-conjugate synthase

Function and homology information

Biological species

Streptomyces rugosporus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.897 Å

Authors

Pan, L. / Guo, Y. / Liu, J.

Funding support

China, 2items

Citation

Journal: Cell Chem Biol / Year: 2016
Title: Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4
Authors: Zheng, Q. / Guo, Y. / Yang, L. / Zhao, Z. / Wu, Z. / Zhang, H. / Liu, J. / Cheng, X. / Wu, J. / Yang, H. / Jiang, H. / Pan, L. / Liu, W.

History

Deposition	Jun 3, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 30, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5bu3.cif.gz	412.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5bu3.ent.gz	345.9 KB	Display	PDB format
PDBx/mmJSON format	5bu3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5bu3_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	5bu3_full_validation.pdf.gz	1.8 MB	Display
Data in XML	5bu3_validation.xml.gz	39.6 KB	Display
Data in CIF	5bu3_validation.cif.gz	55.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bu/5bu3 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/5bu3	HTTPS FTP

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Related structure data

Related structure data	5btuSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3u72-d 3ib1-d 3bih-d 2px1-d 3v5a-d 3rgy-d 6jaw-d 3ttr-d 2o92-d 3d1r-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: PyrI4

B: PyrI4

C: PyrI4

D: PyrI4

hetero molecules

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

1

A: PyrI4

B: PyrI4

hetero molecules

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

2

C: PyrI4

D: PyrI4

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.121, 91.030, 112.876
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PyrI4 Mass: 19499.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces rugosporus (bacteria) / Gene: pyrI4 / Plasmid: pET28a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: K7QVW7
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Formula: C₃H₈O₃
#3: Chemical	ChemComp-4W9 / (4S,4aS,6aS,8R,9R,10aR,13R,14aS,18aR,18bR)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,5,6,6a,7,8,9,10,10a,13,14,18a,18b-hexadecahydro-1H-14a,17-(metheno)benzo[b]naphtho[2,1-h]azacyclododecine-16,18(15H,17H)-dione Mass: 499.682 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₀H₄₅NO₅
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 717 / 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: 2.53 Å³/Da / Density % sol: 51.46 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.04M Citric acid, 0.06M Bis-Tris propane pH 6.4, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 28, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.897→50 Å / Num. obs: 63379 / % possible obs: 99.9 % / Observed criterion σ(I): 3.25 / Redundancy: 11.3 % / R_merge(I) obs: 0.105 / Net I/σ(I): 17.03
Reflection shell	Resolution: 1.897→1.93 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 4.54 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
HKL-3000		data processing
PHENIX	1.8.2_1309	phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5BTU

5btu

Resolution: 1.897→39.198 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.204	3112	5.11 %
R_work	0.1613	-	-
obs	0.1635	60912	95.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.897→39.198 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5364	0	192	717	6273

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	5665
X-RAY DIFFRACTION	f_angle_d	1.916	7741
X-RAY DIFFRACTION	f_dihedral_angle_d	14.774	2085
X-RAY DIFFRACTION	f_chiral_restr	0.298	917
X-RAY DIFFRACTION	f_plane_restr	0.009	994

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 (%)
1.8974-1.9271	0.2419	123	0.1918	1864	X-RAY DIFFRACTION	69
1.9271-1.9587	0.2541	120	0.1882	2094	X-RAY DIFFRACTION	78
1.9587-1.9925	0.2148	108	0.1777	2251	X-RAY DIFFRACTION	83
1.9925-2.0287	0.2321	138	0.1759	2467	X-RAY DIFFRACTION	91
2.0287-2.0677	0.2198	134	0.1714	2563	X-RAY DIFFRACTION	96
2.0677-2.1099	0.2509	133	0.1776	2690	X-RAY DIFFRACTION	98
2.1099-2.1558	0.2247	129	0.1673	2638	X-RAY DIFFRACTION	98
2.1558-2.2059	0.2223	160	0.1681	2718	X-RAY DIFFRACTION	99
2.2059-2.2611	0.2309	136	0.1604	2712	X-RAY DIFFRACTION	100
2.2611-2.3222	0.2072	145	0.1532	2711	X-RAY DIFFRACTION	100
2.3222-2.3905	0.1879	123	0.1509	2747	X-RAY DIFFRACTION	100
2.3905-2.4677	0.1847	154	0.1477	2711	X-RAY DIFFRACTION	100
2.4677-2.5559	0.215	138	0.1516	2731	X-RAY DIFFRACTION	100
2.5559-2.6582	0.1867	158	0.1529	2719	X-RAY DIFFRACTION	100
2.6582-2.7791	0.2148	157	0.1631	2738	X-RAY DIFFRACTION	100
2.7791-2.9256	0.2298	168	0.165	2697	X-RAY DIFFRACTION	100
2.9256-3.1088	0.2029	161	0.1647	2745	X-RAY DIFFRACTION	100
3.1088-3.3488	0.1957	151	0.1592	2765	X-RAY DIFFRACTION	100
3.3488-3.6855	0.1856	147	0.1548	2751	X-RAY DIFFRACTION	100
3.6855-4.2183	0.195	135	0.1466	2799	X-RAY DIFFRACTION	100
4.2183-5.3125	0.1394	158	0.1376	2785	X-RAY DIFFRACTION	99
5.3125-39.206	0.2556	136	0.1967	2904	X-RAY DIFFRACTION	98

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	0.0005	-0	0.0005	0.0027	-0.0017	0.0008	-0.0086	0.0011	-0.0021	-0.0187	-0.0034	0.0041	0.0057	-0.0282	-0.0001	0.1325	0.0105	-0.0147	0.1938	-0.0072	0.1396	-22.4915	9.6652	-41.155
2	0.0099	-0.0009	-0.0001	0.0013	-0.0009	0.0005	-0.0061	0.0008	0.0008	-0.0058	-0.0102	0.0037	-0.0169	0.0031	-0.0011	0.1032	0.0519	0.0044	0.114	0.0183	0.0891	-10.9523	24.5879	-35.7922
3	0.0165	-0	-0.0038	0.0029	0.0114	0.0316	-0.0108	0.0119	0.0119	-0.0565	-0.0411	-0.0572	0.0374	0.0125	-0.0691	0.0142	0.0296	0.1765	0.0169	-0.018	0.0414	-3.5089	9.0512	-36.741
4	0.0247	0.0246	0.0401	0.0264	0.0375	0.0652	-0.031	-0.0044	-0.0238	-0.0407	-0.0511	-0.0049	0.0756	-0.0138	-0.0406	0.0815	0.0661	0.097	0.0682	0.0157	0.0902	-9.0505	8.3829	-31.526
5	0.0323	-0.0201	-0.0129	0.0268	0.0046	0.0075	-0.0231	-0.0067	-0.0263	-0.0105	-0.0028	-0.0147	0.023	0.0153	-0.0109	0.1132	0.0905	0.0554	0.0744	0.0288	0.0794	-1.5672	9.8572	-34.1408
6	0.0431	-0.0026	0.0044	0.0189	-0.0112	0.0083	-0.0191	0.0056	-0.0315	-0.0286	-0.0229	-0.0262	0.0193	-0.0105	-0.0313	0.0601	0.0707	0.0469	0.0892	0.0242	0.0794	-5.3217	12.1629	-39.9291
7	0.0043	0.0005	-0	0.0017	0.0006	0.0004	0.0033	-0.0084	0.0039	0.0043	-0.014	-0.007	-0.0095	0.0013	0.0001	0.1899	-0.0055	-0.053	0.1149	0.0139	0.1689	-1.0579	36.033	-16.4273
8	0.0015	0.0004	0.001	0.0039	0.0007	0.0021	0	-0.0081	-0.0067	0.0071	-0.011	0.0016	0.0035	-0.0077	-0.0008	0.1211	0.0511	0.0124	0.1269	0.0219	0.0965	-15.1559	25.8168	-22.8995
9	0.0013	-0.0013	0.0012	0.001	-0.0011	0.001	-0.0018	-0.0012	-0.0146	-0.0033	-0.0007	0.003	0.0035	0.008	0.0008	0.1149	0.0039	0.0125	0.0954	0.0254	0.1238	-10.9933	1.1152	-18.2283
10	0.0001	-0.0001	0.0002	0.0004	-0.0005	0.001	0.0073	-0.0123	-0.0084	0.0043	0.0066	0.0117	0.0022	-0.0073	-0	0.1752	-0.0305	-0.0218	0.2081	0.1022	0.1613	-10.2065	5.5563	-9.7208
11	0.0007	0.0007	0.0007	0.0008	0.0001	0.0009	-0.0074	-0.0008	0.0068	0.0038	0.0027	-0.0146	-0.0105	0.0018	-0	0.2478	0.0101	-0.0324	0.1812	0.032	0.1627	3.1092	28.1191	-12.4636
12	0.0002	-0.0003	-0.0006	0.0007	0.0003	0.006	-0.0005	0.0058	-0.0021	0.0009	-0.0005	-0.0014	-0.0007	-0.0003	-0.0001	0.1877	-0.0408	-0.0042	0.176	0.0551	0.1749	9.5704	32.3833	-29.7702
13	0.0012	0.0011	-0.0012	0.0007	-0.0008	0.0017	-0.0123	-0.0204	0.0151	0.0165	0.0041	-0.0172	-0.0041	-0.0149	0	0.1415	0.0244	0.002	0.1418	0.0071	0.0958	0.8699	24.0602	-9.0675
14	0.0047	-0.0008	0.0047	0.0074	0.0041	0.0081	0.0179	-0.0452	-0.0095	0.0063	-0.0061	-0.0263	-0.0156	0.002	0.0169	0.0876	0.0223	-0.0225	0.0692	0.0904	0.1068	3.1678	22.1542	-19.4978
15	0.0069	0.0034	0.001	0.0114	0.0005	0.0008	0.0163	-0.0222	-0.0321	0.0235	-0.0298	-0.0439	-0.0105	0.0058	-0.0047	0.0615	0.0465	-0.0278	0.0494	0.0904	0.1107	-1.5371	16.6921	-18.6947
16	0.0125	0.0087	-0.0076	0.0057	-0.0059	0.0117	0.0079	-0.0433	-0.0062	0.0239	-0.0242	-0.008	-0.0527	0.0014	0.0029	0.1434	0.0183	-0.0235	0.0839	0.0352	0.1043	-5.6168	19.7898	-13.5308
17	0.0066	0.0049	-0.0038	0.0068	-0.0019	0.0064	0.0043	0.0105	0.0034	-0.0023	0.0065	-0.007	0.0115	-0.0013	0.0025	0.2491	-0.0391	0.0746	0.2407	-0.1239	0.1782	-39.2373	-13.6751	-39.8337
18	0.0073	0.0023	0.003	0.0012	-0.0013	0.0055	-0.0156	0.0413	0.0163	-0.0058	-0.0156	-0.0062	0.019	-0.0357	-0.0048	0.1014	-0.054	0.004	0.089	0.0231	0.1125	-51.4229	6.7199	-24.1844
19	0.0138	0.0158	0.0073	0.0397	0.0197	0.0247	-0.0723	0.1945	0.027	-0.1253	0.0601	-0.0326	0.0015	0.0259	-0.0142	0.0375	-0.1004	0.0777	0.0994	0.0714	0.0658	-39.164	0.3448	-31.5265
20	0.0021	-0.0002	-0.0005	0.0008	-0	0.0002	0.0016	0.0039	0.007	0.0076	0.0069	0.0116	-0.0007	-0.013	0	0.0927	-0.0205	0.0135	0.1549	0.0097	0.149	-63.1717	-1.998	-6.663
21	0.0024	-0.0033	-0.0012	0.0054	0.0017	0.002	-0.0033	0.0035	0.0131	-0.0146	-0.0039	-0.0269	0.0374	-0.0074	-0.0005	0.0528	-0.0199	-0.0192	0.0679	0.0164	0.1165	-41.9319	-10.0183	-16.4358
22	0.0004	-0.0006	0.0006	0.004	0	0.0013	0.0017	-0.0022	0.0023	-0.0001	0	-0.0017	0.0081	0.0018	-0.0001	0.1927	-0.004	-0.0034	0.2415	-0.001	0.2524	-23.8349	-8.226	-16.865
23	0.0012	-0.0006	-0.0004	0.0008	-0.0004	0.0001	0.0046	-0.0021	-0.0052	-0.0029	0.0087	-0.0091	0.015	0.0067	0	0.113	-0.0136	-0.0613	0.128	0.0547	0.2326	-30.5926	-8.6186	-7.3392
24	0.0267	0.0214	-0.0172	0.0166	-0.0118	0.012	0.0492	0.0267	0.0353	0.0485	0	0.0262	0.0093	-0.0501	0.0193	0.1082	0.0049	-0.0452	0.1121	0.0255	0.0799	-53.8202	3.5323	-4.9601
25	0.0066	0.011	-0.0028	0.0187	-0.0023	0.0013	0.0026	0.0133	0.0159	0.0411	0.0326	-0.0057	0.0141	-0.0157	0.0224	0.0672	-0.0221	-0.0867	0.1036	0.0357	0.0454	-49.7011	4.5377	-10.5312
26	0.0062	-0.0065	-0.0014	0.0139	-0.0029	0.002	-0.0191	-0.0164	0.0172	0.0328	-0.0068	-0.0369	-0.0158	0.0015	-0.0149	0.0707	-0.0574	-0.0791	0.0784	0.0236	0.0803	-43.6426	0.9006	-11.565
27	0.0192	-0.0008	-0.0017	0.0119	-0.0012	0.0086	-0.0076	-0.01	0.015	0.0271	0.0055	-0.0268	0.0004	0.0105	0.0017	0.0384	-0.0358	-0.054	0.0898	0.0411	0.0723	-45.9176	-4.6818	-7.4157

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 29 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 30 through 108 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 109 through 140 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 141 through 156 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 157 through 184 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 18 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 19 through 29 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 30 through 49 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 50 through 62 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 63 through 73 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 74 through 81 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 82 through 95 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 96 through 125 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 126 through 156 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 157 through 184 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 4 through 18 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 19 through 49 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 50 through 184 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 4 through 19 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 20 through 40 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 41 through 49 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 50 through 62 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 63 through 95 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 96 through 125 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 126 through 156 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 157 through 184 )

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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

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

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Jul 12, 2017. Major update of PDB

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Yorodumi