PDB-3tfz: Crystal structure of Zhui aromatase/cyclase from Streptomcyes sp....

ID or keywords:

Entry

Database: PDB / ID: 3tfz

Title

Crystal structure of Zhui aromatase/cyclase from Streptomcyes sp. R1128

Components

Cyclase

Keywords

BIOSYNTHETIC PROTEIN / HELIX-GRIP / BET V1-LIKE SUPERFAMILY / AROMATIC POLYKETIDE CYCLASE/DEHYDRASE

Function / homology

Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / : / Cyclase

Function and homology information

Biological species

Streptomyces sp. R1128 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.39 Å

Authors

Ames, B.D. / Lee, M.Y. / Moody, C. / Zhang, W. / Tang, Y. / Wong, S.K. / Tsai, S.C.

Citation

Journal: Biochemistry / Year: 2011
Title: Structural and Biochemical Characterization of ZhuI Aromatase/Cyclase from the R1128 Polyketide Pathway.
Authors: Ames, B.D. / Lee, M.Y. / Moody, C. / Zhang, W. / Tang, Y. / Tsai, S.C.

History

Deposition	Aug 16, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 14, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2011	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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	3tfz.cif.gz	401.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3tfz.ent.gz	332 KB	Display	PDB format
PDBx/mmJSON format	3tfz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3tfz_validation.pdf.gz	505.1 KB	Display	wwPDB validaton report
Full document	3tfz_full_validation.pdf.gz	555.9 KB	Display
Data in XML	3tfz_validation.xml.gz	45.1 KB	Display
Data in CIF	3tfz_validation.cif.gz	59.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/3tfz ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tfz	HTTPS FTP

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Related structure data

Similar structure data	2i1s-d 1ii5-1 4xb0-d 4jhi-1 1y1a-d 6f6d-d 3mc1-3 1tq8-2 5f64-1 4gxd-1 Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cyclase

B: Cyclase

C: Cyclase

D: Cyclase

E: Cyclase

F: Cyclase

hetero molecules

115 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cyclase

B: Cyclase

hetero molecules

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

2

C: Cyclase

D: Cyclase

hetero molecules

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

3

E: Cyclase

F: Cyclase

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.016, 135.731, 175.496
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cyclase / R1128 POLYKETIDE AROMATASE/CYCLASE ZHUI Mass: 18799.078 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. R1128 (bacteria) / Gene: zhuI / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F6D3
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID Mass: 221.317 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₉H₁₉NO₃S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.64 Å³/Da / Density % sol: 53.42 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.1M NAH2PO4/0.7M K2PO4, 0.1M CAPS PH 10.5, 0.2M LI2SO4, 0.1M NACITRATE, 0.1M GUANIDINE HCL, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength	Wavelength (Å)
SYNCHROTRON	SSRL	BL7-1	1	0.97607
SYNCHROTRON	ALS	8.2.2	2		0.97903, 0.97923, 0.96104

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315r	1	CCD	Mar 8, 2008
ADSC QUANTUM 315	2	CCD	Apr 15, 2009

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL, SI(111)	SINGLE WAVELENGTH	M	x-ray	1
2	KOHZU MONOCHROMATOR, DOUBLE CRYSTAL, SI(111)	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97607	1
2	0.97903	1
3	0.97923	1
4	0.96104	1

Reflection

Resolution: 2.39→50 Å / Num. obs: 48090 / % possible obs: 99.8 % / Redundancy: 7 % / R_sym value: 0.128 / Net I/σ(I): 16.4

Reflection shell

Resolution: 2.39→2.49 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.7 / R_sym value: 0.466 / % possible all: 99

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
SOLVE		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.39→50 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.903 / SU B: 15.596 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.261	2430	5.1 %	RANDOM
R_work	0.193	-	-	-
obs	0.196	45669	99.3 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 43.222 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.06 Å²	0 Å²	0 Å²
2-	-	1.21 Å²	0 Å²
3-	-	-	-0.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.39→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7675	0	102	168	7945

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.028	0.021	7909
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.518	1.958	10769
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.325	5	981
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.67	23.085	389
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.101	15	1247
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.685	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.21	0.2	1247
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6026
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	3180
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	5001
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	349
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.204	0.2	10
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.254	0.2	60
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.229	0.2	14
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.116	1.5	4910
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.948	2	7900
X-RAY DIFFRACTION	r_scbond_it	3.452	3	3017
X-RAY DIFFRACTION	r_scangle_it	5.254	4.5	2869
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.39→2.45 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	170	-
R_work	0.22	2979	-
obs	-	-	90.99 %

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	3.4567	0.4632	-0.2484	1.5946	-0.4551	3.0637	0.076	0.2071	0.1918	-0.1396	-0.0535	0.1042	-0.0542	0.054	-0.0225	-0.0592	0.0208	-0.0155	-0.0751	-0.0615	-0.0372	-10.7327	-4.5033	4.2446
2	4.5672	0.4317	0.3216	3.1266	0.5003	5.6836	0.0194	0.4748	0.3663	-0.2735	0.057	0.2834	-0.0647	-0.2071	-0.0764	0.0179	0.0248	-0.0164	0.0027	0.0596	0.0565	-18.2209	2.1111	-0.4539
3	5.6911	1.4474	2.6499	1.8483	0.9121	2.8004	0.0173	0.1962	0.0156	-0.0602	0.024	0.2484	0.0739	-0.0298	-0.0413	-0.016	0.0113	0.0027	-0.0853	-0.0196	-0.0236	-23.2834	-10.1965	3.1229
4	11.2765	3.7803	-1.7954	4.4724	-1.302	2.6606	-0.1618	0.3469	-0.0322	-0.1828	0.0519	-0.3427	-0.0331	0.3486	0.11	0.0047	0.0286	-0.029	0.0549	-0.0229	-0.0443	0.7749	-6.0383	0.2859
5	3.8139	-1.6396	-0.457	2.5862	0.1535	3.7399	-0.1581	-0.4729	-0.5453	0.189	0.2059	0.0903	0.5707	0.2138	-0.0477	0.0828	0.0122	-0.0001	0.0385	0.0002	0.0548	-8.2958	-23.1426	26.4587
6	4.7778	0.0547	-0.9154	6.0458	2.0737	4.3924	-0.1304	-0.176	-0.2781	-0.2062	0.187	-0.1331	0.5143	0.2219	-0.0566	0.0935	0.0551	-0.0432	0.1402	0.0514	-0.0329	-2.4527	-24.5676	24.431
7	1.5759	-2.5394	-1.3095	9.0516	4.0802	2.3903	-0.1742	-0.0659	-0.3134	0.2166	0.1753	0.0793	0.2052	0.1436	-0.0011	0.029	0.0224	-0.0057	0.0178	-0.0207	-0.0171	-6.0226	-27.1051	13.9508
8	5.3033	-1.0376	-2.4661	6.9623	3.8539	7.8137	-0.0342	-0.5279	-0.0265	0.6094	0.0484	0.4936	0.1723	-0.2106	-0.0142	0.0682	-0.0008	0.018	0.0341	0.0338	0.0669	-19.9792	-17.6174	26.9443
9	5.4799	-0.3216	-0.0559	2.9125	0.6574	5.689	-0.038	0.3918	0.3623	-0.2818	-0.0831	0.4694	-0.2137	-0.9132	0.1211	0.0767	0.0916	-0.0251	0.2098	-0.1394	0.2327	-29.8435	13.7167	21.4772
10	9.6043	0.4875	-3.9615	5.6792	3.0383	11.1843	0.3607	-0.4416	2.0233	-1.4337	-0.2693	1.5131	-2.4049	-0.8567	-0.0915	0.5427	0.3901	-0.2206	0.4998	-0.1618	0.6983	-32.6873	24.2401	14.3296
11	5.3321	0.3554	0.0956	4.4214	1.9453	2.3947	0.0423	0.1485	0.4321	-0.5081	-0.059	0.252	-0.071	-0.1418	0.0167	-0.0172	0.056	0.021	0.085	-0.1478	0.146	-23.7063	11.9382	19.2977
12	3.1374	0.7166	0.3598	5.9219	-0.9192	4.8082	-0.0617	0.2156	0.6843	-0.1085	-0.1748	0.1011	-0.9808	-0.3975	0.2366	0.2474	0.1498	-0.0773	0.1373	-0.1342	0.3359	-24.5549	24.5274	21.4017
13	5.7372	-1.2603	0.3188	2.1506	0.7162	6.7417	-0.16	-1.1824	0.4366	0.2977	0.3592	-0.2236	-0.3275	0.8693	-0.1992	0.1307	-0.0654	0.0163	0.3879	-0.2252	0.1355	-4.0307	13.076	40.0078
14	13.2597	7.9747	9.2944	83.0042	-8.5597	18.3566	0.3276	1.0804	1.4534	-2.0985	0.2604	-0.1012	0.489	-1.0974	-0.5881	0.6341	0.1312	0.1466	0.7617	0.1766	0.5375	-1.0658	24.8432	47.0805
15	7.8066	-3.0355	3.0819	3.0563	-4.1115	5.7405	-0.5553	-1.2984	0.9869	0.9984	0.3834	-0.2001	-0.5227	-0.0889	0.1718	0.2902	0.0137	-0.0609	0.5397	-0.2421	0.1989	-9.8284	13.4568	47.2395
16	3.2301	-0.068	-0.0418	3.6285	0.8465	3.316	-0.095	-0.6786	0.9057	0.2979	0.213	-0.1184	-0.7099	0.3239	-0.118	0.2282	-0.0196	-0.0656	0.256	-0.2493	0.3366	-10.3262	20.4465	38.0961
17	77.3241	-41.7125	-60.2175	32.6209	42.4984	56.8056	-0.7737	-1.3747	1.2218	1.0835	1.1129	1.8878	0.6213	-0.0368	-0.3392	0.3644	-0.05	0.0068	0.374	0.1876	0.3371	-12.2818	14.4666	-8.6603
18	3.4232	-0.409	1.5092	1.858	-1.9255	4.8283	-0.0481	0.1393	-0.0528	0.1226	-0.0903	-0.2237	-0.3286	0.4375	0.1384	-0.0167	-0.0222	-0.0019	0.1595	0.0297	0.0265	8.8237	5.7842	-15.3515
19	4.2123	-0.4534	0.4988	2.4114	-1.9792	3.4148	0.152	0.0583	-0.0546	0.0717	-0.0764	-0.0348	0.1331	0.0578	-0.0756	-0.0708	-0.0256	-0.0128	0.0989	0.0297	-0.0191	-0.9511	5.1203	-17.4597
20	5.8301	-1.9509	-3.7716	4.9364	3.8839	13.8988	0.0554	-0.4646	0.8448	0.5901	0.1947	-0.1828	-0.8009	0.5077	-0.25	0.2288	-0.0882	-0.0563	0.1667	-0.003	0.1419	2.4739	16.6552	-12.9735
21	3.2467	-1.0093	1.7024	1.8264	-0.7207	5.2557	-0.0348	0.0977	0.128	-0.0087	-0.0296	0.0775	-0.4017	-0.7117	0.0644	0.0039	0.0456	0.053	0.3844	0.0353	-0.047	-18.98	13.1545	-33.3686
22	3.9495	-0.3858	2.1454	5.9312	-2.0778	5.2242	-0.22	0.0447	0.3024	0.3981	0.0589	0.2072	-0.5464	-0.4981	0.1611	0.0639	0.0617	0.0114	0.5113	0.0534	-0.0273	-19.6193	16.2952	-40.916
23	3.1044	-1.3413	1.4962	4.2951	-1.8469	7.0233	-0.132	0.2395	0.4284	-0.0655	-0.0667	-0.1103	-1.0174	-0.1592	0.1987	0.0432	0.0093	-0.0213	0.3263	0.0365	-0.0188	-11.2735	19.3723	-36.323
24	4.2981	5.6086	-0.7331	12.8211	-3.8021	6.3148	-0.133	-0.1803	0.4047	0.689	0.1637	0.1035	-1.1573	-0.4666	-0.0307	0.1748	0.1531	-0.0203	0.3714	-0.0075	0.0761	-16.1104	21.2426	-27.7969

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 34
2	X-RAY DIFFRACTION	2	A	35 - 78
3	X-RAY DIFFRACTION	3	A	79 - 141
4	X-RAY DIFFRACTION	4	A	142 - 167
5	X-RAY DIFFRACTION	5	B	0 - 55
6	X-RAY DIFFRACTION	6	B	56 - 81
7	X-RAY DIFFRACTION	7	B	82 - 140
8	X-RAY DIFFRACTION	8	B	141 - 164
9	X-RAY DIFFRACTION	9	C	0 - 46
10	X-RAY DIFFRACTION	10	C	47 - 62
11	X-RAY DIFFRACTION	11	C	63 - 104
12	X-RAY DIFFRACTION	12	C	105 - 163
13	X-RAY DIFFRACTION	13	D	0 - 48
14	X-RAY DIFFRACTION	14	D	49 - 63
15	X-RAY DIFFRACTION	15	D	64 - 90
16	X-RAY DIFFRACTION	16	D	91 - 163
17	X-RAY DIFFRACTION	17	E	-2 - 3
18	X-RAY DIFFRACTION	18	E	4 - 66
19	X-RAY DIFFRACTION	19	E	67 - 113
20	X-RAY DIFFRACTION	20	E	114 - 162
21	X-RAY DIFFRACTION	21	F	0 - 41
22	X-RAY DIFFRACTION	22	F	42 - 73
23	X-RAY DIFFRACTION	23	F	74 - 124
24	X-RAY DIFFRACTION	24	F	125 - 160

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