PDB-6zry: 6-dimethylallyl tryptophan synthase

ID or keywords:

Entry

Database: PDB / ID: 6zry

Title

6-dimethylallyl tryptophan synthase

Components

DMATS type aromatic prenyltransferase

Keywords

TRANSFERASE /

Complex / ABBA-barrel fold /

Prenyltransferase

Function / homology

Aromatic prenyltransferase, DMATS-type /

Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / DI(HYDROXYETHYL)ETHER /

TRYPTOPHAN / DMATS type aromatic prenyltransferase

Function and homology information

Biological species

Micromonospora olivasterospora (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.652 Å

Authors

Ostertag, E. / Stehle, T. / Zocher, G.

Funding support

Germany, 1items

Citation

Journal: J.Mol.Biol. / Year: 2020
Title: Reprogramming Substrate and Catalytic Promiscuity of Tryptophan Prenyltransferases.
Authors: Ostertag, E. / Zheng, L. / Broger, K. / Stehle, T. / Li, S.M. / Zocher, G.

History

Deposition	Jul 15, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6zry.cif.gz	268.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6zry.ent.gz		Display	PDB format
PDBx/mmJSON format	6zry.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zr/6zry ftp://data.pdbj.org/pub/pdb/validation_reports/zr/6zry	HTTPS FTP

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Related structure data

Related structure data	6zrxC 6zrzC 6zs0C 5injS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6zrx-2 4boj-2 3vxd-4 2ahf-1 1qno-d 4yzk-d 6xzl-d 4w85-2 4oou-1 3wh9-2 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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

AAA: DMATS type aromatic prenyltransferase

BBB: DMATS type aromatic prenyltransferase

hetero molecules

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

1

AAA: DMATS type aromatic prenyltransferase

hetero molecules

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

2

BBB: DMATS type aromatic prenyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.355, 85.682, 74.538
Angle α, β, γ (deg.)	90.000, 99.764, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DMATS type aromatic prenyltransferase Mass: 40546.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora olivasterospora (bacteria) Gene: MolI14.36, JD77_02062 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MFY2
#2: Chemical	ChemComp-TRP / TRYPTOPHAN / Tryptophan Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.18 Å³/Da / Density % sol: 43.55 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 200 mM Calcium acetate, 26% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00767 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 17, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00767 Å / Relative weight: 1
Reflection	Resolution: 1.65→46.7 Å / Num. obs: 78991 / % possible obs: 99.8 % / Redundancy: 4.5 % / B_iso Wilson estimate: 27.7 Å² / CC_1/2: 0.99 / R_rim(I) all: 0.1 / Net I/σ(I): 10.9
Reflection shell	Resolution: 1.65→1.75 Å / Num. unique obs: 12658 / CC_1/2: 0.64 / R_rim(I) all: 1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XSCALE		data scaling
PHASER	7.1.001	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5INJ

5inj

Resolution: 1.652→46.667 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.947 / WR_factor R_free: 0.207 / WR_factor R_work: 0.17 / SU B: 6.265 / SU ML: 0.099 / Average fsc free: 0.8501 / Average fsc work: 0.8648 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2185	1580	2 %
R_work	0.1858	77405	-
all	0.186	-	-
obs	-	78985	99.786 %

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: 24.054 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.791 Å²	0 Å²	1.129 Å²
2-	-	-1.285 Å²	-0 Å²
3-	-	-	0.099 Å²

Refinement step

Cycle: LAST / Resolution: 1.652→46.667 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5350	0	79	588	6017

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	5649
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	5287
X-RAY DIFFRACTION	r_angle_refined_deg	1.442	1.65	7698
X-RAY DIFFRACTION	r_angle_other_deg	1.335	1.575	12169
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.204	5	723
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.425	19.216	319
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.387	15	819
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.17	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	696
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6503
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1305
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	1135
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	5024
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	2740
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2553
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	484
X-RAY DIFFRACTION	r_metal_ion_refined	0.072	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.244	0.2	41
X-RAY DIFFRACTION	r_nbd_other	0.22	0.2	135
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.15	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	1.095	1.897	2868
X-RAY DIFFRACTION	r_mcbond_other	1.095	1.897	2867
X-RAY DIFFRACTION	r_mcangle_it	1.908	2.836	3590
X-RAY DIFFRACTION	r_mcangle_other	1.908	2.836	3591
X-RAY DIFFRACTION	r_scbond_it	1.186	2.103	2781
X-RAY DIFFRACTION	r_scbond_other	1.186	2.104	2782
X-RAY DIFFRACTION	r_scangle_it	1.985	3.068	4105
X-RAY DIFFRACTION	r_scangle_other	1.985	3.069	4106
X-RAY DIFFRACTION	r_lrange_it	5.065	24.026	6424
X-RAY DIFFRACTION	r_lrange_other	5.064	24.03	6425

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
1.652-1.695	0.353	115	0.343	5643	0.343	5821	0.515	0.537	98.9177	0.321
1.695-1.741	0.315	114	0.303	5568	0.303	5685	0.635	0.696	99.9472	0.274
1.741-1.792	0.309	110	0.293	5415	0.293	5527	0.711	0.725	99.9638	0.26
1.792-1.847	0.279	107	0.259	5233	0.26	5347	0.819	0.825	99.8691	0.224
1.847-1.907	0.244	105	0.236	5147	0.236	5255	0.86	0.862	99.9429	0.197
1.907-1.974	0.24	100	0.216	4900	0.216	5003	0.89	0.896	99.94	0.179
1.974-2.048	0.26	97	0.199	4741	0.201	4853	0.892	0.909	99.6909	0.168
2.048-2.132	0.207	93	0.186	4587	0.186	4683	0.928	0.931	99.9359	0.157
2.132-2.226	0.227	90	0.183	4380	0.183	4477	0.911	0.933	99.8436	0.159
2.226-2.335	0.234	86	0.177	4215	0.178	4303	0.929	0.934	99.9535	0.154
2.335-2.461	0.188	81	0.161	3995	0.161	4081	0.949	0.954	99.8775	0.139
2.461-2.61	0.208	77	0.151	3782	0.152	3863	0.944	0.96	99.8965	0.133
2.61-2.789	0.216	73	0.166	3564	0.167	3638	0.94	0.952	99.9725	0.149
2.789-3.012	0.22	67	0.172	3292	0.173	3369	0.93	0.947	99.7032	0.16
3.012-3.298	0.215	63	0.175	3066	0.176	3132	0.919	0.948	99.9042	0.167
3.298-3.685	0.228	56	0.166	2768	0.167	2828	0.942	0.958	99.8586	0.165
3.685-4.25	0.127	51	0.14	2459	0.14	2515	0.978	0.975	99.8012	0.146
4.25-5.195	0.164	42	0.146	2083	0.146	2127	0.975	0.974	99.906	0.161
5.195-7.302	0.235	33	0.205	1626	0.206	1659	0.945	0.942	100	0.219
7.302-46.667	0.253	20	0.193	941	0.194	964	0.938	0.955	99.6888	0.233

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	0.3581	0.1713	0.076	0.9898	-0.1933	0.5563	-0.0531	0.0121	0.008	0.0139	0.0178	0.0336	0.0768	-0.0584	0.0353	0.0299	-0.0119	0.0122	0.0343	0.0046	0.0383	-6.0058	3.8215	40.6591
2	0.1959	0.0083	-0.377	0.2638	-0.037	0.7492	-0.0812	0.0053	-0.0052	-0.1005	0.0352	-0.0303	0.1862	0.0035	0.0461	0.0865	-0.0003	0.039	0.0175	0.0179	0.0505	7.5987	2.9613	25.014
3	0.1862	0.1795	-0.3729	0.5872	-0.1086	0.904	0.0053	0.0051	0.0024	0.0027	-0.0051	-0.0126	-0.0081	-0.0033	-0.0002	0.017	-0.0007	0.0235	0.04	0.0218	0.0665	8.5117	18.1135	25.2171
4	0.153	0.0125	-0.316	0.4679	-0.1284	0.7392	0.0227	-0.0002	0.013	0.0286	0.0086	-0.0411	-0.1107	0.0302	-0.0313	0.0684	-0.0102	0.0263	0.0359	0.0098	0.0325	3.4632	23.5882	33.5731
5	0.4026	0.0098	-0.1671	0.645	-0.3205	0.3325	0.0331	0.0536	0.0269	0.0806	0.0271	0.046	-0.0348	-0.0302	-0.0602	0.0396	0.0135	0.0319	0.045	0.0164	0.0468	-5.1594	18.4801	42.7974
6	0.137	0.2126	0.0407	1.0644	0.1741	0.0375	-0.0081	-0.0327	0.0452	0.0547	0.0302	0.0145	-0.0006	0.0023	-0.0222	0.0394	0.0069	0.023	0.0196	-0.0155	0.0856	11.933	13.5171	72.6208
7	0.2539	0.2926	0.1056	0.9087	0.4555	0.5608	-0.0028	-0.0196	0.0775	-0.1154	0.0554	-0.1057	-0.0512	-0.0088	-0.0526	0.039	-0.0072	0.0503	0.0236	-0.029	0.1019	25.7995	12.1723	58.6926
8	2.5664	1.9559	1.836	3.3248	3.2646	7.4041	0.2876	0.0664	-0.0586	-0.0659	-0.1248	-0.16	0.3515	0.0304	-0.1628	0.1219	0.0514	0.0112	0.0247	0.0093	0.0089	19.9932	-0.5446	46.0071
9	0.4133	-0.1188	-0.1584	0.3972	0.0999	0.1714	-0.0129	0.0123	-0.0302	-0.0448	0.053	-0.0177	0.0292	0.0165	-0.04	0.0416	0.0005	0.0183	0.0261	-0.0053	0.0585	19.8616	-5.5818	61.2136
10	0.3975	-0.0483	-0.1297	1.0387	-0.1188	0.2581	-0.0116	-0.0045	0.02	0.0645	0.0592	0.071	0.0394	0.0243	-0.0476	0.0373	0.0099	0.0235	0.032	0.0116	0.0486	7.4495	-3.2786	72.0968

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 88
2	X-RAY DIFFRACTION	2	ALL	AAA	89 - 190
3	X-RAY DIFFRACTION	3	ALL	AAA	191 - 243
4	X-RAY DIFFRACTION	4	ALL	AAA	244 - 302
5	X-RAY DIFFRACTION	5	ALL	AAA	303 - 357
6	X-RAY DIFFRACTION	6	ALL	BBB	2 - 104
7	X-RAY DIFFRACTION	7	ALL	BBB	105 - 183
8	X-RAY DIFFRACTION	8	ALL	BBB	184 - 195
9	X-RAY DIFFRACTION	9	ALL	BBB	196 - 303
10	X-RAY DIFFRACTION	10	ALL	BBB	304 - 358

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