PDB-8su5: F198T epi-Isozizaene Synthase: complex with 3 Mg2+, inorganic pyr...

ID or keywords:

Entry

Database: PDB / ID: 8su5

Title

F198T epi-Isozizaene Synthase: complex with 3 Mg2+, inorganic pyrophosphate, and benzyl triethyl ammonium cation

Components

Epi-isozizaene synthase

Keywords

LYASE / Terpene / Terpenoid / Isoprenoid / Terpene cyclase / Terpene synthase

Function / homology

Function and homology information

epi-isozizaene synthase / epi-isozizaene synthase activity / terpene synthase activity / metal ion binding
Similarity search - Function

Biological species

Streptomyces coelicolor A3

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.48 Å

Authors

Eaton, S.A. / Christianson, D.W.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2023
Title: Reprogramming the Cyclization Cascade of epi -Isozizaene Synthase to Generate Alternative Terpene Products.
Authors: Eaton, S.A. / Christianson, D.W.

History

Deposition	May 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 26, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 16, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8su5.cif.gz	179.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8su5.ent.gz	121.5 KB	Display	PDB format
PDBx/mmJSON format	8su5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8su5_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	8su5_full_validation.pdf.gz	2.8 MB	Display
Data in XML	8su5_validation.xml.gz	17.1 KB	Display
Data in CIF	8su5_validation.cif.gz	25.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/su/8su5 ftp://data.pdbj.org/pub/pdb/validation_reports/su/8su5	HTTPS FTP

-
Related structure data

Related structure data	8su0C 8su1C 8su2C 8su3C 8su4C C: citing same article (ref.)
Similar structure data	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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #201 - Sep 2016 Isoprene Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1)

Deposited unit

A: Epi-isozizaene synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	53.261, 47.238, 75.154
Angle α, β, γ (deg.)	90.000, 95.394, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

-
Protein , 1 types, 1 molecules A

#1: Protein	Epi-isozizaene synthase / EIZS / Sesquiterpene cyclase / Sesquiterpene synthase Mass: 43669.941 Da / Num. of mol.: 1 / Mutation: F198T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: cyc1, SCO5222, SC7E4.19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K499, epi-isozizaene synthase

#1: Protein

Epi-isozizaene synthase / EIZS / Sesquiterpene cyclase / Sesquiterpene synthase

Mass: 43669.941 Da / Num. of mol.: 1 / Mutation: F198T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptomyces coelicolor A3(2) (bacteria)
Gene: cyc1, SCO5222, SC7E4.19 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K499, epi-isozizaene synthase

-
Non-polymers , 6 types, 294 molecules

#2: Chemical	ChemComp-BTM / N-benzyl-N,N-diethylethanaminium Mass: 192.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₂N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₂O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 42.93 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris (pH 6.3), 200 mM (NH4)2SO4, 30% (w/v) PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.48→29.33 Å / Num. obs: 116473 / % possible obs: 99.5 % / Redundancy: 3.4 % / B_iso Wilson estimate: 15.85 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / Net I/σ(I): 12.4
Reflection shell	Resolution: 1.48→1.51 Å / R_merge(I) obs: 0.632 / Mean I/σ(I) obs: 2 / Num. unique obs: 2826 / CC_1/2: 0.72

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
PHENIX	1.14_3260	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.48→29.33 Å / SU ML: 0.1621 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.384 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1787	3776	3.24 %
R_work	0.1676	112697	-
obs	0.1679	116473	96.22 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.48→29.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2702	0	37	287	3026

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0119	2822
X-RAY DIFFRACTION	f_angle_d	1.2221	3856
X-RAY DIFFRACTION	f_chiral_restr	0.0899	407
X-RAY DIFFRACTION	f_plane_restr	0.0087	495
X-RAY DIFFRACTION	f_dihedral_angle_d	19.1201	984

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 (%)
1.48-1.5	0.3154	129	0.2876	3594	X-RAY DIFFRACTION	84.29
1.5-1.52	0.313	135	0.2653	4103	X-RAY DIFFRACTION	94.68
1.52-1.54	0.2634	140	0.2567	4095	X-RAY DIFFRACTION	95.23
1.54-1.56	0.2578	140	0.2398	4207	X-RAY DIFFRACTION	95.66
1.56-1.59	0.2631	141	0.2339	4146	X-RAY DIFFRACTION	95.54
1.59-1.61	0.2718	142	0.2234	4154	X-RAY DIFFRACTION	95.3
1.61-1.64	0.2188	140	0.2125	4122	X-RAY DIFFRACTION	95.45
1.64-1.67	0.2364	141	0.204	4195	X-RAY DIFFRACTION	96.33
1.67-1.7	0.2028	141	0.1896	4129	X-RAY DIFFRACTION	95.08
1.7-1.73	0.2363	135	0.1806	4169	X-RAY DIFFRACTION	96.42
1.73-1.76	0.2133	137	0.1797	4175	X-RAY DIFFRACTION	96.81
1.76-1.8	0.2417	143	0.1805	4209	X-RAY DIFFRACTION	97.12
1.8-1.84	0.1905	139	0.1748	4256	X-RAY DIFFRACTION	97.06
1.84-1.89	0.2048	144	0.1704	4234	X-RAY DIFFRACTION	97.07
1.89-1.94	0.205	139	0.1659	4153	X-RAY DIFFRACTION	96.95
1.94-2	0.1777	142	0.1679	4205	X-RAY DIFFRACTION	97.07
2-2.06	0.1856	139	0.1616	4227	X-RAY DIFFRACTION	97.07
2.06-2.14	0.1752	140	0.1601	4224	X-RAY DIFFRACTION	96.44
2.14-2.22	0.1694	135	0.1594	4183	X-RAY DIFFRACTION	95.89
2.22-2.32	0.1507	145	0.1495	4188	X-RAY DIFFRACTION	97.44
2.32-2.45	0.1616	138	0.1585	4189	X-RAY DIFFRACTION	96.78
2.45-2.6	0.1648	144	0.165	4286	X-RAY DIFFRACTION	98.69
2.6-2.8	0.2081	139	0.1703	4275	X-RAY DIFFRACTION	98.42
2.8-3.08	0.1923	141	0.1747	4280	X-RAY DIFFRACTION	98.53
3.08-3.53	0.1506	141	0.1628	4231	X-RAY DIFFRACTION	97.63
3.53-4.44	0.1397	141	0.1343	4228	X-RAY DIFFRACTION	96.98
4.44-29.33	0.1374	145	0.1461	4240	X-RAY DIFFRACTION	98.08

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	1.86387339756	-1.25885820189	0.35726131625	3.33234414205	0.278091491025	1.64759830411	0.0938434246785	0.188980199094	0.0256974560497	-0.219083027706	-0.0535676639189	-0.170266723564	-0.0895207226923	0.210026250114	-0.0427468073857	0.118867400817	-0.016637904767	0.0162651963221	0.174081212274	0.0144400664032	0.131931214126	7.76290196136	4.79737104126	2.32677457849
2	0.799515896217	-0.278185788449	-1.45739763378	1.54598136262	0.684616572231	2.85868646073	0.125678783402	-0.203553058927	0.153054849185	0.135407232235	-0.0350645927916	-0.117500379455	-0.432164003185	0.350487525782	-0.0595638204533	0.263371530463	-0.0619406188181	-0.0122680684773	0.151930420288	-0.0185199138236	0.191479512337	8.7022941096	16.9933754021	22.6293325858
3	1.17144388362	0.136790736691	0.46992325081	0.497812824231	-0.41223476454	3.67118288936	0.0345995830564	-0.0354998152214	-0.00110429124488	0.0403055409529	-0.0408778807985	-0.00173703861049	-0.0618480992308	0.0923364463745	0.0164461686506	0.105491574446	-0.0047514498418	-0.00114924238079	0.0653188392112	-0.00155404043286	0.113753651083	3.18693249439	7.15197896681	20.7846519595
4	3.24052488893	-0.669259221248	0.426608351197	1.62190350474	-0.226506699475	3.10077464916	-0.0213170090539	-0.282816208625	-0.0710739436601	0.241998665126	-0.0847831605249	-0.0549357208998	0.129699446486	0.271058702552	0.0830070516941	0.188749128987	0.000622969030466	0.00196842306059	0.120033105036	0.0187545803451	0.114032407018	3.03347396606	-1.22112059242	36.9716911373
5	2.18062607789	-0.071145590164	0.754231355113	0.960851050637	0.0116724386248	2.84985848103	-0.00394352573441	-0.18198783496	0.059564370676	0.12876336751	-0.0418548869747	-0.0116596607534	-0.179536593883	-0.217872521065	0.0829464216775	0.171820281436	0.0154813189129	0.00891378937838	0.113097682031	-0.0222631360981	0.154556295188	-5.76964266348	9.83851058465	31.1529541762
6	3.96429705844	-1.13710371169	0.892396506608	1.28983610125	-0.393614327957	2.57557129066	0.00676588844509	-0.142030968834	-0.0821492674526	0.0954628690671	-0.0803011472303	-0.0412539758433	0.391725545826	0.0301973182268	0.0310028294733	0.187116563169	-0.00188021890315	0.017720194494	0.0853324829219	0.0197646673817	0.12244275953	-1.61449123634	-5.27944833012	27.6165227967
7	1.62059727377	-1.02114538911	-0.141687292501	2.27443950837	-0.549462670616	0.543211283411	-0.198549126537	-0.0957661273055	-0.278669120375	-0.0670011637215	0.0755788840023	-0.172276989502	0.842662397754	0.126215828306	-0.0358097853312	0.391577071003	0.0814880406745	0.0511012919423	0.121630259842	0.0140329804109	0.219101501659	5.35115045463	-12.6380745372	20.3998425857
8	1.5593828571	-0.0690134244028	0.473175039093	1.72948314257	0.202436582558	2.58014864693	-0.0542802649084	0.011076600711	-0.0808066773622	0.0436777842767	-0.0326335679044	0.154186801761	0.233932387534	-0.440402222254	0.101778825121	0.121684289101	-0.0244026648729	0.0231970681332	0.17075906376	-0.0143710818107	0.131608028362	-11.8368936701	-0.575329863764	14.5049259682
9	3.79914981855	-0.192283253772	0.450886542524	0.803180461256	0.156303238649	1.76340338293	-0.0820900657503	0.0506104099585	-0.190874360287	0.0411656337205	0.0250907277986	-0.030851998317	0.273274635957	0.136251436587	0.0126400264291	0.148775916187	0.0226795631945	0.0116957709535	0.083540586497	-0.00170970150636	0.116085127893	5.45760304457	-5.85924880828	11.8338089982
10	0.475220504034	-0.402514667098	-0.510871826249	1.55940876081	-0.236254261164	0.928563272429	-0.00275726602965	-0.0212893371189	-0.2992950289	0.21767292912	0.114681176569	-0.344523542549	1.24183903691	1.0709092203	-0.169969859481	0.468375609593	0.281402676945	-0.000258045498883	0.40576728583	-0.00931161533877	0.272812613403	16.0949901417	-14.4891360792	18.2777231413
11	4.68243292115	-1.77944120661	0.196620030663	1.47411610558	0.101369084554	2.75658441695	0.027889487071	0.112568108126	-0.108642287522	-0.0198092640912	0.00325970909776	-0.0217851267234	0.314687064303	0.0780075920477	-0.0403002724613	0.173959129519	-0.0202328044628	-0.00151674424405	0.0798416604342	-0.0276634118778	0.141201056604	-0.174352233806	-8.42802802095	2.59024077437
12	4.17394490042	0.542246382041	0.661008056406	0.862765614887	-0.208889630784	1.73121505133	-0.087081159105	0.0928756843781	0.0929163740538	-0.0653699176241	0.0498657982739	0.0905470638902	0.00506621036914	-0.222032307315	0.0400432440408	0.105988335634	-0.0031894888556	-0.0102528580357	0.108612969751	-0.00741262625002	0.102610126561	-6.2338453436	3.49891679182	5.88168511628
13	4.05525802278	-0.0359613268529	1.18229035611	2.73553909883	-0.520971666124	1.81854828703	-0.112820543001	-0.217366874471	0.139616067809	0.183098298241	-0.0198799656428	-0.407970229015	-0.0326572181756	0.720413052549	0.0940934241927	0.128651237614	0.00351052023991	-0.0238948770493	0.308518140993	0.00890720476076	0.196134231657	20.524503829	4.87476986873	21.5830716208

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 107 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 108 through 126 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 127 through 154 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 155 through 181 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 182 through 199 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 200 through 222 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 223 through 250 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 251 through 268 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 269 through 301 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 302 through 335 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 336 through 355 )

-
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

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 6 types, 294 molecules

-
Details

-
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

-Protein , 1 types, 1 molecules A

-Non-polymers , 6 types, 294 molecules

-Details

-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

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 6 types, 294 molecules

-
Details

-
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