PDB-6zs0: Crystal structure of 5-dimethylallyltryptophan synthase from Stre...

ID or keywords:

Entry

Database: PDB / ID: 6zs0

Title

Crystal structure of 5-dimethylallyltryptophan synthase from Streptomyces coelicolor

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 / DMATS type aromatic prenyltransferase

Function and homology information

Biological species

Streptomyces coelicolor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Ostertag, E. / Broger, K. / 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

-
Download

PDBx/mmCIF format	6zs0.cif.gz	265.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6zs0.ent.gz		Display	PDB format
PDBx/mmJSON format	6zs0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zs/6zs0 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zs0	HTTPS FTP

-
Related structure data

Related structure data	6zrxC 6zryC 6zrzC 5injS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6zrz-1 6xso-1 1zsw-d 3r1m-d 1g5c-3 4is9-2 1g5c-2 2zfi-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: DMATS type aromatic prenyltransferase

BBB: DMATS type aromatic prenyltransferase

hetero molecules

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

1

AAA: DMATS type aromatic prenyltransferase

defined by author
Evidence: gel filtration
39.7 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
39.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.880, 70.454, 91.145
Angle α, β, γ (deg.)	90.000, 92.946, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DMATS type aromatic prenyltransferase Mass: 39683.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: FHV93_101284 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4R8NF71
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 1.85 Å³/Da / Density % sol: 33.4 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 150 mM Bis-tris 23% PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 1.5→45.5 Å / Num. obs: 88635 / % possible obs: 97.7 % / Redundancy: 4.6 % / B_iso Wilson estimate: 27.7 Å² / CC_1/2: 0.99 / R_rim(I) all: 0.01 / Net I/σ(I): 15.4
Reflection shell	Resolution: 1.5→1.59 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 14007 / CC_1/2: 0.61

-
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: 1.5→41.055 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.953 / WR_factor R_free: 0.209 / WR_factor R_work: 0.176 / SU B: 4.622 / SU ML: 0.081 / Average fsc free: 0.877 / Average fsc work: 0.8826 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2199	1773	2 %
R_work	0.1891	86857	-
all	0.19	-	-
obs	-	88630	97.692 %

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: 23.913 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.064 Å²	0 Å²	0.016 Å²
2-	-	0.478 Å²	-0 Å²
3-	-	-	-0.54 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→41.055 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5227	0	14	524	5765

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	5603
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	5153
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	1.649	7689
X-RAY DIFFRACTION	r_angle_other_deg	1.385	1.57	11885
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.543	5	765
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.075	18.866	291
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.789	15	786
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.52	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	715
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6609
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1288
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	1191
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	4698
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	2748
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2432
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	381
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.088	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.314	0.2	48
X-RAY DIFFRACTION	r_nbd_other	0.249	0.2	170
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.195	0.2	43
X-RAY DIFFRACTION	r_mcbond_it	1.005	1.609	2949
X-RAY DIFFRACTION	r_mcbond_other	1.005	1.608	2948
X-RAY DIFFRACTION	r_mcangle_it	1.747	2.401	3721
X-RAY DIFFRACTION	r_mcangle_other	1.747	2.401	3722
X-RAY DIFFRACTION	r_scbond_it	1.119	1.765	2654
X-RAY DIFFRACTION	r_scbond_other	1.119	1.766	2655
X-RAY DIFFRACTION	r_scangle_it	1.877	2.593	3958
X-RAY DIFFRACTION	r_scangle_other	1.876	2.594	3959
X-RAY DIFFRACTION	r_lrange_it	5.215	20.59	6331
X-RAY DIFFRACTION	r_lrange_other	5.151	20.389	6291

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
1.5-1.539	0.333	128	0.348	6252	0.348	6685	0.586	0.599	95.4375	0.345
1.539-1.581	0.316	124	0.298	6120	0.299	6472	0.768	0.781	96.4771	0.284
1.581-1.627	0.294	124	0.275	6032	0.275	6354	0.823	0.805	96.8839	0.255
1.627-1.677	0.258	119	0.259	5853	0.259	6157	0.844	0.842	96.9953	0.231
1.677-1.732	0.253	116	0.24	5674	0.241	5950	0.891	0.885	97.3109	0.211
1.732-1.792	0.242	112	0.23	5524	0.23	5782	0.894	0.896	97.4749	0.198
1.792-1.86	0.254	109	0.217	5332	0.218	5566	0.899	0.915	97.7542	0.187
1.86-1.936	0.258	105	0.22	5118	0.221	5350	0.904	0.904	97.6262	0.19
1.936-2.022	0.249	100	0.195	4918	0.196	5131	0.915	0.932	97.7977	0.168
2.022-2.12	0.218	97	0.187	4726	0.188	4939	0.939	0.946	97.6513	0.164
2.12-2.234	0.201	92	0.171	4516	0.172	4684	0.947	0.953	98.3775	0.152
2.234-2.369	0.241	87	0.185	4276	0.186	4433	0.93	0.943	98.4209	0.163
2.369-2.532	0.218	83	0.184	4042	0.185	4173	0.936	0.94	98.8497	0.165
2.532-2.734	0.226	76	0.178	3743	0.179	3867	0.939	0.948	98.7587	0.162
2.734-2.994	0.197	71	0.164	3491	0.165	3604	0.956	0.96	98.8346	0.156
2.994-3.345	0.199	64	0.171	3143	0.172	3233	0.945	0.952	99.1958	0.169
3.345-3.859	0.228	57	0.161	2786	0.162	2869	0.933	0.959	99.0938	0.167
3.859-4.715	0.162	49	0.15	2372	0.15	2450	0.97	0.971	98.8163	0.164
4.715-6.625	0.177	38	0.189	1860	0.189	1913	0.956	0.961	99.2159	0.213
6.625-41.055	0.229	22	0.178	1079	0.179	1108	0.944	0.963	99.3682	0.212

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	1.3008	-0.9968	-0.4346	0.7931	0.207	0.7887	0.0345	0.0393	0.0734	-0.0644	-0.0034	-0.0711	0.1513	-0.1708	-0.0311	0.0731	-0.0154	0.0009	0.1031	0.0089	0.0705	10.3535	-4.6715	-2.9977
2	0.1833	0.2002	-0.2233	0.255	-0.1318	0.7561	0.0265	0.0419	0.0036	0.0308	0.0419	-0.0391	-0.0807	-0.0701	-0.0684	0.0612	0.0264	-0.0069	0.0766	0.0149	0.0979	13.2794	10.7849	9.1498
3	0.1575	0.0866	-0.0333	1.0084	-0.9289	2.4685	-0.0477	-0.0629	0.0734	0.1501	0.0719	-0.037	-0.2548	-0.272	-0.0242	0.0828	0.0894	-0.0053	0.1098	0.0045	0.0658	3.0732	8.0213	22.9366
4	0.4923	0.0172	0.0474	0.4328	0.0807	0.2227	-0.0542	0.016	0.0171	0.1328	0.1493	-0.0876	-0.0003	-0.1839	-0.0951	0.05	0.0647	-0.0216	0.2725	0.0554	0.0512	2.7967	0.0332	21.8904
5	0.4445	-0.1753	0.4839	1.1705	0.4584	0.9657	-0.0338	-0.1208	-0.0233	-0.0394	0.1402	-0.0672	-0.0285	-0.1791	-0.1064	0.0277	-0.0623	-0.0161	0.2319	0.0612	0.0263	-1.5749	-5.4185	12.9841
6	1.6316	-1.326	-0.5578	1.0797	0.4647	0.2981	-0.1205	-0.1588	-0.2317	0.1042	0.1132	0.1859	0.1183	-0.0202	0.0074	0.1401	-0.0254	-0.0055	0.1022	0.0466	0.1165	13.8274	-19.7841	6.7759
7	0.2738	0.0162	-0.0788	0.3842	-0.3186	0.7642	0.0176	-0.0115	0.0013	0.0941	-0.0366	-0.0086	-0.0922	0.0522	0.0191	0.0874	-0.0367	-0.0127	0.0724	0.0256	0.0782	28.5286	-20.3708	44.6957
8	0.7528	-0.264	-0.1377	0.4427	-0.255	0.5951	0.0925	0.0889	0.0651	0.0283	-0.1123	-0.012	0.1086	0.1024	0.0199	0.128	0.0225	0.0162	0.0891	0.0363	0.0759	36.1224	-33.9476	38.9306
9	0.5282	0.3146	0.9383	1.2636	-0.1666	2.1883	0.1581	0.1278	0.0149	-0.0517	-0.1097	0.0874	0.325	0.316	-0.0484	0.143	0.1247	0.0284	0.1168	0.0136	0.0252	34.6703	-38.5272	23.3209
10	0.4359	0.2917	0.7178	1.8242	-1.2273	3.0443	0.0391	0.01	0.0412	-0.1311	-0.1001	0.0934	0.254	0.1658	0.061	0.0747	0.0453	0.035	0.073	0.0112	0.0746	27.0371	-28.934	20.3314
11	0.254	-0.3341	0.1172	0.5698	0.1501	0.7678	0.0078	0.0152	0.0025	-0.0139	-0.0175	0.0011	0.0031	0.0018	0.0097	0.0793	0.0012	0.0188	0.0591	-0.0053	0.087	21.8758	-17.6982	25.764
12	2.8733	2.1503	1.8761	1.7235	1.7438	2.2845	0.0007	-0.083	-0.1881	0.0296	-0.0729	-0.0919	0.0528	-0.0571	0.0722	0.0819	-0.0269	0.0139	0.0473	0.0084	0.1178	22.5685	-22.1028	32.1186

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	1 - 55
2	X-RAY DIFFRACTION	2	ALL	AAA	56 - 192
3	X-RAY DIFFRACTION	3	ALL	AAA	193 - 242
4	X-RAY DIFFRACTION	4	ALL	AAA	243 - 298
5	X-RAY DIFFRACTION	5	ALL	AAA	299 - 341
6	X-RAY DIFFRACTION	6	ALL	AAA	342 - 359
7	X-RAY DIFFRACTION	7	ALL	BBB	2 - 79
8	X-RAY DIFFRACTION	8	ALL	BBB	80 - 158
9	X-RAY DIFFRACTION	9	ALL	BBB	159 - 197
10	X-RAY DIFFRACTION	10	ALL	BBB	198 - 222
11	X-RAY DIFFRACTION	11	ALL	BBB	223 - 330
12	X-RAY DIFFRACTION	12	ALL	BBB	331 - 351

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi