PDB-8su4: F198S epi-Isozizaene Synthase: complex with 3 Mg2+, inorganic pyr...

ID or keywords:

Entry

Database: PDB / ID: 8su4

Title

F198S 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: 1.43 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

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Download

PDBx/mmCIF format	8su4.cif.gz	191.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8su4.ent.gz	123.4 KB	Display	PDB format
PDBx/mmJSON format	8su4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8su4_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	8su4_full_validation.pdf.gz	2.8 MB	Display
Data in XML	8su4_validation.xml.gz	15.9 KB	Display
Data in CIF	8su4_validation.cif.gz	23.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/su/8su4 ftp://data.pdbj.org/pub/pdb/validation_reports/su/8su4	HTTPS FTP

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Related structure data

Related structure data	8su0C 8su1C 8su2C 8su3C 8su5C C: citing same article (ref.)
Similar structure data	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	#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

44.5 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)	52.883, 46.987, 75.530
Angle α, β, γ (deg.)	90.000, 95.865, 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

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Protein , 1 types, 1 molecules A

#1: Protein	Epi-isozizaene synthase / EIZS / Sesquiterpene cyclase / Sesquiterpene synthase Mass: 43655.918 Da / Num. of mol.: 1 / Mutation: F198S 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: 43655.918 Da / Num. of mol.: 1 / Mutation: F198S
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

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Non-polymers , 6 types, 214 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₂O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.14 Å³/Da / Density % sol: 42.48 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris (pH 6.4), 200 mM (NH4)2SO4, 28% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.43→75.13 Å / Num. obs: 67562 / % possible obs: 98.9 % / Redundancy: 3.3 % / B_iso Wilson estimate: 20 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.038 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.43→1.45 Å / R_merge(I) obs: 0.806 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3292 / CC_1/2: 0.719

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.43→75.13 Å / SU ML: 0.1616 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3947 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1894	3358	4.98 %
R_work	0.1716	64130	-
obs	0.1724	67488	98.65 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.43→75.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2721	0	49	205	2975

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0093	2896
X-RAY DIFFRACTION	f_angle_d	1.0448	3959
X-RAY DIFFRACTION	f_chiral_restr	0.0855	415
X-RAY DIFFRACTION	f_plane_restr	0.0079	510
X-RAY DIFFRACTION	f_dihedral_angle_d	18.1283	1038

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 (%)
1.43-1.45	0.3514	150	0.366	2623	X-RAY DIFFRACTION	97.95
1.45-1.47	0.3774	155	0.348	2645	X-RAY DIFFRACTION	98.73
1.47-1.49	0.3124	140	0.3238	2604	X-RAY DIFFRACTION	98.53
1.49-1.52	0.3277	138	0.2929	2694	X-RAY DIFFRACTION	98.54
1.52-1.55	0.3177	138	0.2722	2638	X-RAY DIFFRACTION	99.04
1.55-1.57	0.2734	131	0.2531	2679	X-RAY DIFFRACTION	98.74
1.57-1.6	0.2351	135	0.233	2710	X-RAY DIFFRACTION	98.89
1.6-1.64	0.2448	138	0.2175	2607	X-RAY DIFFRACTION	98.25
1.64-1.67	0.2021	138	0.2023	2662	X-RAY DIFFRACTION	98.7
1.67-1.71	0.2258	140	0.1908	2689	X-RAY DIFFRACTION	99.4
1.71-1.75	0.2129	143	0.1814	2672	X-RAY DIFFRACTION	99.15
1.75-1.8	0.2179	135	0.1727	2673	X-RAY DIFFRACTION	99.12
1.8-1.85	0.1773	142	0.1705	2684	X-RAY DIFFRACTION	99.09
1.85-1.91	0.1665	142	0.1625	2664	X-RAY DIFFRACTION	99.12
1.91-1.98	0.1894	139	0.1671	2676	X-RAY DIFFRACTION	98.74
1.98-2.06	0.1751	131	0.1725	2679	X-RAY DIFFRACTION	98.77
2.06-2.16	0.1941	167	0.1606	2660	X-RAY DIFFRACTION	98.85
2.16-2.27	0.1703	127	0.1541	2664	X-RAY DIFFRACTION	98.24
2.27-2.41	0.1948	142	0.1609	2698	X-RAY DIFFRACTION	98.78
2.41-2.6	0.1934	145	0.1634	2672	X-RAY DIFFRACTION	99.26
2.6-2.86	0.1986	139	0.1677	2683	X-RAY DIFFRACTION	98.57
2.86-3.27	0.1701	131	0.1656	2703	X-RAY DIFFRACTION	98.3
3.27-4.12	0.1493	129	0.1469	2721	X-RAY DIFFRACTION	98.07
4.12-75.13	0.1746	143	0.1564	2730	X-RAY DIFFRACTION	96.83

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	1.61417465861	-1.97329052011	-0.589419622331	5.05477171095	1.68984219535	2.01916440171	0.110040505253	0.137391929865	0.0205441438397	-0.193202012055	-0.101326598689	-0.0751623984119	-0.140667504012	0.154799372843	0.00934483174706	0.163752861266	-0.0114444369353	-0.0187673144028	0.255760976418	0.022110080048	0.194084757855	7.33974343253	4.03873908535	2.43206602553
2	2.40139807342	-0.836335066868	-1.29185940592	1.79072279705	0.16057951526	4.41371795912	0.0856666637468	-0.312080915276	0.266312175646	0.224389224344	-0.00171727034201	-0.135148538372	-0.290581161699	0.368313427016	-0.0683033378208	0.339318425106	-0.0587154992767	-0.0273504539099	0.242702101043	-0.0380749413663	0.287087004477	8.50923271872	16.0948451393	23.1028595659
3	2.15104076868	-0.927886563326	1.39578908053	1.84298728114	-1.12398315741	4.99592730581	-0.010253623445	-0.0406816644055	-0.0715755916668	0.23071752117	0.00813329302093	0.0721698982802	0.0193276788399	0.0771505493417	0.0173470714691	0.205724914802	-0.015088724664	0.00201512698851	0.161074649228	-0.0106547044139	0.190159875076	3.02019445271	6.21789731761	20.8952300165
4	1.66526545217	-0.882504371155	0.298218684447	1.92226603212	-0.275981663112	3.09605173849	-0.0987920428088	-0.132583637658	0.00796482786063	0.541719229844	-0.0198333314906	0.0549969185633	-0.0268759282912	0.030910135114	0.109170717467	0.358418926741	-0.0136883153024	0.0425442165861	0.197591898282	-0.0172305212712	0.219536237257	-2.48447860933	4.3280076384	33.7902313515
5	3.28262938103	-0.497327274745	0.48709295759	1.64193647877	-0.0168256284767	2.97701087201	0.0543587685963	-0.0917397799284	0.00297293152065	0.425099835099	-0.135662419405	0.0952550739115	0.573667989665	-0.000374682435511	0.0436427646867	0.438195700012	-0.0215751536286	0.0744258219056	0.181549656025	-0.001819931491	0.231625135667	-1.9992540324	-6.05028069754	27.5640072897
6	1.83163985374	0.349536157761	-0.916567430891	3.1920411373	-0.358645080159	1.41758551121	-0.251227928629	-0.0711415610184	-0.212480424066	0.21025390301	0.130757510223	-0.155147666563	1.03486278857	0.150450122534	0.0221496332482	0.588483104389	0.0654014375792	0.0511438277564	0.226796984781	0.00672981422886	0.260506536284	5.1315941655	-13.8745909002	20.7312417738
7	1.94163625551	-0.360629585111	0.0975060019823	1.70489865591	0.368337412469	2.07240014989	-0.0878711757721	0.0168120375812	-0.140052951275	0.220354386264	-0.013906693499	0.13033104945	0.264171373497	-0.0620382934793	0.092294797892	0.204107897889	-0.0195935449874	0.0268885887623	0.159928086944	-0.00833500664302	0.183203628904	-2.46832979942	-4.42274300526	13.203039617
8	3.88638565602	-1.62024234975	-1.54254460252	4.33946863528	-0.462075787191	0.953511956555	-0.1786097962	-0.182684099045	-0.373960902134	0.681321327281	0.195395362269	-0.423610664297	1.31161723648	1.0227921272	-0.0949983124832	0.579882505321	0.243079641341	-0.0365530708277	0.410860897965	0.024920058525	0.335294827045	15.7973877634	-15.3608673599	18.3291513264
9	2.36463985014	-2.49932626233	1.39670423688	3.38959585047	-0.448203510212	3.66540561334	0.00399645856466	0.320270466731	-0.182238103267	0.0682840812114	-0.0371338984874	0.0413880854986	0.336208181028	0.182385240802	-0.0366546220754	0.198340107621	-0.0247248361802	0.000954366688173	0.154285336147	-0.0112824625141	0.192501868345	0.24146870878	-9.54743771732	2.70697793449
10	6.13832899406	0.546886306273	1.10485957615	1.3536906922	0.0651504488966	1.58659441516	-0.0643877592455	-0.0167097707253	0.135808942323	0.0332019513604	-0.0198296441846	0.147629903966	0.0374540166279	-0.157834671413	0.0821682071494	0.165647470558	-0.0122985684633	-0.00884598579405	0.212437472476	-0.0160111357243	0.216761304742	-6.31724517492	2.62303532547	5.88697335205
11	6.28445323208	-0.0098418803698	1.83446842684	4.71154042141	-0.831999230551	6.7151287325	0.047067039626	-0.216331403924	-0.00158804137324	0.265374055916	0.00364865869859	-0.778948351288	0.0166159419921	0.976707521286	-0.0661578062833	0.200138640661	0.0180282370259	-0.0493466272935	0.3642463103	-0.0310927499914	0.317603820581	20.3355465407	3.94868124015	21.9471851043

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 154 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 155 through 181 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 182 through 199 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 200 through 250 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 251 through 268 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 269 through 301 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 302 through 335 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 336 through 355 )

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