PDB-6eow: Structure of Raspberry Ketone Synthase with Hydroxybenzalacetone

ID or keywords:

Entry

Database: PDB / ID: 6eow

Title

Structure of Raspberry Ketone Synthase with Hydroxybenzalacetone

Components

Ketone/zingerone synthase 1

Keywords

TRANSFERASE / Raspberry Ketone / Hydroxybenzalacetone / Complex / Synthetic Biology

Function / homology

Function and homology information

2-alkenal reductase [NAD(P)+] activity / nucleotide binding
Similarity search - Function

Biological species

Rubus idaeus (European raspberry)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Tosi, T. / Moore, S.J. / Freemont, P.S.

Citation

Journal: Biorxiv / Year: 2018
Title: A cell-free synthetic biochemistry platform for raspberry ketone production
Authors: Moore, S.J. / Tosi, T. / Hleba, Y.B. / Bell, D. / Polizzi, K.M. / Freemont, P.S.

History

Deposition	Oct 10, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6eow.cif.gz	543.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6eow.ent.gz	446.9 KB	Display	PDB format
PDBx/mmJSON format	6eow.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6eow_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	6eow_full_validation.pdf.gz	1.5 MB	Display
Data in XML	6eow_validation.xml.gz	57 KB	Display
Data in CIF	6eow_validation.cif.gz	78.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eo/6eow ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eow	HTTPS FTP

-
Related structure data

Related structure data	4hfjS S: Starting model for refinement
Similar structure data	3a17-3 2j3i-d 2j3h-d 3a17-2 2j3j-d 1dbt-d 3a16-2 6n0z-3 3a17-1 3a18-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (5) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Ketone/zingerone synthase 1

B: Ketone/zingerone synthase 1

C: Ketone/zingerone synthase 1

D: Ketone/zingerone synthase 1

hetero molecules

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

1

A: Ketone/zingerone synthase 1

B: Ketone/zingerone synthase 1

hetero molecules

defined by author&software
Evidence: gel filtration
83.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Ketone/zingerone synthase 1

hetero molecules

D: Ketone/zingerone synthase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.038, 81.733, 93.046
Angle α, β, γ (deg.)	77.68, 85.13, 72.70
Int Tables number	1
Space group name H-M	P1

#1: Protein	Ketone/zingerone synthase 1 Mass: 40703.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rubus idaeus (European raspberry) / Gene: ZS1 / Production host: Escherichia coli (E. coli) / References: UniProt: G1FCG0
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-BKZ / 4-(4-hydroxyphenyl)butan-2-one Mass: 164.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 605 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.42 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES/imidazole pH 6.3, 11% (w/v) PEG 550 MME and 5% (w/v) PEG 20K, 20 mM of amino acid mixture

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97936 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97936 Å / Relative weight: 1
Reflection	Resolution: 1.8→29.11 Å / Num. obs: 121687 / % possible obs: 97.4 % / Redundancy: 3.5 % / R_merge(I) obs: 0.037 / Net I/σ(I): 18.8
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.145 / Mean I/σ(I) obs: 6.5 / CC_1/2: 0.965 / R_rim(I) all: 0.206 / % possible all: 96

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HFJ

4hfj

Resolution: 1.8→29.11 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / Phase error: 18.47

	R_factor	Num. reflection	% reflection
R_free	0.1872	6025	4.95 %
R_work	0.1615	-	-
obs	0.1627	121680	97.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.8→29.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10370	0	228	605	11203

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	10906
X-RAY DIFFRACTION	f_angle_d	1.576	14786
X-RAY DIFFRACTION	f_dihedral_angle_d	6.465	8797
X-RAY DIFFRACTION	f_chiral_restr	0.312	1610
X-RAY DIFFRACTION	f_plane_restr	0.007	1862

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 (%)
1.8-1.8205	0.2268	187	0.1874	3862	X-RAY DIFFRACTION	96
1.8205-1.8419	0.2028	181	0.1736	3774	X-RAY DIFFRACTION	96
1.8419-1.8643	0.1992	189	0.1702	3839	X-RAY DIFFRACTION	96
1.8643-1.8879	0.1985	218	0.1666	3809	X-RAY DIFFRACTION	96
1.8879-1.9128	0.1913	198	0.1622	3784	X-RAY DIFFRACTION	96
1.9128-1.939	0.1996	204	0.1599	3807	X-RAY DIFFRACTION	97
1.939-1.9667	0.2009	192	0.1554	3857	X-RAY DIFFRACTION	97
1.9667-1.996	0.1987	193	0.156	3796	X-RAY DIFFRACTION	96
1.996-2.0272	0.1961	181	0.1494	3891	X-RAY DIFFRACTION	97
2.0272-2.0604	0.1791	211	0.1599	3790	X-RAY DIFFRACTION	97
2.0604-2.0959	0.1908	197	0.1596	3844	X-RAY DIFFRACTION	97
2.0959-2.134	0.209	204	0.1651	3865	X-RAY DIFFRACTION	97
2.134-2.1751	0.2139	200	0.1652	3781	X-RAY DIFFRACTION	97
2.1751-2.2195	0.1866	215	0.1578	3885	X-RAY DIFFRACTION	97
2.2195-2.2677	0.179	194	0.156	3878	X-RAY DIFFRACTION	97
2.2677-2.3204	0.1971	193	0.1622	3849	X-RAY DIFFRACTION	97
2.3204-2.3784	0.1822	194	0.1591	3830	X-RAY DIFFRACTION	98
2.3784-2.4427	0.1948	209	0.1617	3888	X-RAY DIFFRACTION	98
2.4427-2.5145	0.2162	210	0.1701	3822	X-RAY DIFFRACTION	98
2.5145-2.5957	0.2089	224	0.1669	3884	X-RAY DIFFRACTION	98
2.5957-2.6884	0.1929	214	0.1681	3865	X-RAY DIFFRACTION	98
2.6884-2.7959	0.1991	180	0.1648	3891	X-RAY DIFFRACTION	98
2.7959-2.9231	0.2045	201	0.1648	3900	X-RAY DIFFRACTION	98
2.9231-3.077	0.1875	209	0.1735	3896	X-RAY DIFFRACTION	98
3.077-3.2695	0.1879	182	0.1706	3921	X-RAY DIFFRACTION	98
3.2695-3.5216	0.1913	218	0.1677	3877	X-RAY DIFFRACTION	99
3.5216-3.8753	0.1806	198	0.1572	3873	X-RAY DIFFRACTION	99
3.8753-4.4343	0.1694	221	0.1406	3900	X-RAY DIFFRACTION	99
4.4343-5.5803	0.1605	211	0.147	3905	X-RAY DIFFRACTION	99
5.5803-29.1184	0.1798	197	0.1776	3892	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	0.9903	0.2793	0.3416	1.0987	-0.2026	1.0121	-0.0149	-0.3603	0.2956	0.0597	-0.0906	-0.2091	-0.1547	-0.0307	0.0172	0.2699	-0.0472	-0.0428	0.3625	-0.0995	0.2786	3.7537	-24.4287	37.7542
2	0.989	0.0412	0.1017	0.7445	0.2368	1.6268	0.031	-0.1506	0.0437	-0.0033	-0.1202	0.1757	-0.0519	-0.3439	0.0635	0.1803	-0.0075	-0.0292	0.2386	-0.0317	0.2601	-18.1927	-33.5256	16.3599
3	2.9615	-0.6364	-1.552	1.4116	0.924	2.3725	0.0201	-0.0813	0.2849	0.1559	-0.0287	-0.0053	-0.4805	-0.0019	-0.0655	0.3895	-0.0646	-0.0182	0.2236	-0.0748	0.3304	-6.3747	-18.793	23.3565
4	0.9295	0.0031	0.1143	0.5997	0.2411	0.919	-0.0441	-0.5301	0.0501	0.2814	-0.0865	0.1806	-0.0511	-0.4451	0.0528	0.2597	-0.0241	0.0108	0.4076	-0.0408	0.1921	-12.8642	-32.9485	37.1294
5	0.358	0.1514	-0.0661	0.6052	0.2419	0.8072	0.1507	0.2966	-0.0614	-0.3672	-0.1165	-0.2697	-0.0526	0.0784	-0.0543	0.4146	0.0809	0.0904	0.3438	-0.0043	0.252	13.621	-1.8294	-16.1292
6	0.8747	0.0121	1.0927	0.0153	-0.0049	1.5115	0.0752	-0.4622	-0.0611	0.1435	0.0133	-0.4092	0.185	0.6193	-0.0216	0.3115	0.0278	0.0647	0.3507	0.0257	0.2904	15.7587	3.1936	1.1487
7	0.5622	-0.1296	-0.3017	0.9276	-0.0373	0.8785	0.0659	0.2208	-0.3142	-0.3509	-0.1476	-0.2386	0.2097	-0.1167	0.0067	0.4506	0.0665	0.0516	0.2991	-0.0723	0.2786	10.3099	-10.6574	-12.636
8	0.8053	-0.2084	-0.3176	1.0296	0.0313	1.5168	0.0145	0.1195	-0.2156	-0.2146	-0.0314	0.1329	0.273	-0.1045	-0.0271	0.2332	-0.0243	-0.0212	0.1867	-0.0122	0.2328	-3.4562	-7.1149	2.2652
9	0.6825	-0.0329	-0.1777	0.8197	-0.374	0.8717	0.0895	0.2334	0.046	-0.1439	-0.0389	0.2201	-0.1487	-0.3386	-0.0469	0.1535	0.0468	-0.0225	0.2333	0.0234	0.2051	-12.58	8.9333	6.5717
10	0.7541	-0.1532	-0.0394	0.5198	0.0203	0.9642	0.0134	-0.0063	0.0831	-0.0795	0.0065	-0.0399	-0.1266	0	-0.0239	0.1574	-0.0031	0.0155	0.1228	0.0106	0.1892	0.5154	8.1505	16.3854
11	3.2176	-0.5159	1.9099	1.1741	-0.0252	2.0311	0.0166	0.0331	-0.2205	-0.2648	0.0498	0.0827	0.3859	-0.2229	-0.0835	0.3514	-0.0421	-0.0293	0.1996	-0.0003	0.3012	-4.2654	-13.0839	3.3265
12	1.0695	-0.1587	-0.1314	0.6131	0.2315	1.0696	0.1251	0.4107	-0.0145	-0.3098	-0.1025	0.0834	-0.1198	-0.3775	-0.0112	0.3086	0.0662	-0.0191	0.3001	0.0016	0.1434	-2.261	2.49	-10.2742
13	1.2733	0.0117	-0.348	0.6673	0.0989	1.6106	0.0708	-0.3915	0.1009	0.2094	0.0938	0.3312	-0.1216	-0.1213	-0.0509	0.3364	-0.0061	0.1084	0.3167	-0.0357	0.2143	-0.1102	14.1266	52.9119
14	0.8836	0.0817	-0.2127	0.8542	0.3966	1.2151	0.032	-0.195	-0.0573	0.1389	0.0111	-0.0557	0.0162	0.1629	-0.0238	0.1472	-0.0148	-0.0044	0.1932	0.0229	0.1751	14.5813	3.3906	35.2458
15	1.3849	-0.4258	0.1034	0.9927	-0.0543	1.5806	0.072	0.3847	0.0237	-0.3089	-0.0376	0.413	-0.1846	-0.2461	-0.0286	0.3961	0.0112	-0.1193	0.3302	-0.0028	0.289	-11.8565	-25.3349	65.4369
16	0.8594	0.233	-0.1378	0.9296	0.5002	1.6897	-0.0539	0.0729	-0.0166	-0.1816	-0.0068	-0.0714	-0.0273	0.1454	0.048	0.2081	0.0076	-0.0157	0.1471	0.0289	0.2187	6.7787	-24.4633	81.98
17	0.4332	0.3018	0.2365	0.6378	0.2532	0.6332	0.1553	-0.497	-0.2136	0.2065	-0.1469	-0.3307	0.179	0.0209	-0.0311	0.3496	-0.0187	-0.0568	0.5158	0.1096	0.2706	2.3676	-42.7447	42.0592
18	1.0085	0.4918	0.6861	1.0683	0.2048	1.0261	0.0064	-0.2998	-0.0608	-0.014	0.0141	-0.1979	0.0013	0.2357	-0.0173	0.1678	-0.0477	-0.025	0.3239	0.0249	0.1992	0.9011	-38.216	34.204

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 83 through 131 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 132 through 288 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 289 through 308 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 309 through 348 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 8 through 57 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 58 through 74 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 75 through 116 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 117 through 171 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 172 through 224 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 225 through 288 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 289 through 308 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 309 through 348 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 9 through 131 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 132 through 348 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 8 through 131 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 132 through 348 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 9 through 46 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 47 through 82 )

-
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