PDB-8su1: F96H epi-Isozizaene Synthase: complex with 3 Mg2+ and pamidronate

ID or keywords:

Entry

Database: PDB / ID: 8su1

Title

F96H epi-Isozizaene Synthase: complex with 3 Mg2+ and pamidronate

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: 1.37 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	8su1.cif.gz	176 KB	Display	PDBx/mmCIF format
PDB format	pdb8su1.ent.gz	119.3 KB	Display	PDB format
PDBx/mmJSON format	8su1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8su1_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	8su1_full_validation.pdf.gz	2.9 MB	Display
Data in XML	8su1_validation.xml.gz	16.1 KB	Display
Data in CIF	8su1_validation.cif.gz	24.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/su/8su1 ftp://data.pdbj.org/pub/pdb/validation_reports/su/8su1	HTTPS FTP

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Related structure data

Related structure data	8su0C 8su2C 8su3C 8su4C 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	#201 - Sep 2016 Isoprene Synthase similarity (1)

Deposited unit

A: Epi-isozizaene synthase

hetero molecules

44.1 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)	51.682, 46.984, 75.537
Angle α, β, γ (deg.)	90.000, 98.138, 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

#1: Protein	Epi-isozizaene synthase / EIZS / Sesquiterpene cyclase / Sesquiterpene synthase Mass: 43706.984 Da / Num. of mol.: 1 / Mutation: F96H 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
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₁₁NO₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.08 Å³/Da / Density % sol: 40.78 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris (pH 7.0), 200 mM (NH4)2SO4, 26% (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-E / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 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: 1.37→74 Å / Num. obs: 74716 / % possible obs: 98.9 % / Redundancy: 3.3 % / B_iso Wilson estimate: 12.88 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.038 / Net I/σ(I): 19.3
Reflection shell	Resolution: 1.37→1.39 Å / R_merge(I) obs: 0.249 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3544 / CC_1/2: 0.927

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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: 1.37→39.78 Å / SU ML: 0.109 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.3298 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1702	3647	4.88 %
R_work	0.1591	71047	-
obs	0.1597	74694	98.81 %

Solvent computation

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

Displacement parameters

B_iso mean: 16.63 Å²

Refinement step

Cycle: LAST / Resolution: 1.37→39.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2709	0	21	268	2998

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0098	2809
X-RAY DIFFRACTION	f_angle_d	1.1827	3841
X-RAY DIFFRACTION	f_chiral_restr	0.0867	406
X-RAY DIFFRACTION	f_plane_restr	0.0082	494
X-RAY DIFFRACTION	f_dihedral_angle_d	18.4201	978

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 (%)
1.37-1.39	0.1831	147	0.1846	2582	X-RAY DIFFRACTION	95.19
1.39-1.41	0.1981	127	0.1798	2667	X-RAY DIFFRACTION	97.9
1.41-1.43	0.2234	138	0.1739	2747	X-RAY DIFFRACTION	98.33
1.43-1.45	0.1648	148	0.1632	2616	X-RAY DIFFRACTION	97.46
1.45-1.47	0.1745	125	0.1596	2779	X-RAY DIFFRACTION	98.57
1.47-1.49	0.1937	152	0.1523	2686	X-RAY DIFFRACTION	99.13
1.49-1.52	0.1518	141	0.1533	2772	X-RAY DIFFRACTION	99.28
1.52-1.55	0.171	137	0.1527	2700	X-RAY DIFFRACTION	99.37
1.55-1.58	0.1638	147	0.1487	2731	X-RAY DIFFRACTION	99.31
1.58-1.61	0.1822	144	0.1448	2729	X-RAY DIFFRACTION	99.48
1.61-1.65	0.1768	146	0.1453	2755	X-RAY DIFFRACTION	99.42
1.65-1.68	0.1719	137	0.1561	2731	X-RAY DIFFRACTION	99.58
1.68-1.73	0.1712	137	0.1504	2728	X-RAY DIFFRACTION	99.31
1.73-1.77	0.1589	131	0.1569	2767	X-RAY DIFFRACTION	99.31
1.77-1.82	0.1668	129	0.1601	2736	X-RAY DIFFRACTION	99
1.82-1.88	0.1643	135	0.1607	2767	X-RAY DIFFRACTION	99.35
1.88-1.95	0.1929	132	0.1573	2746	X-RAY DIFFRACTION	99.17
1.95-2.03	0.1695	162	0.162	2706	X-RAY DIFFRACTION	99.03
2.03-2.12	0.1766	119	0.1612	2785	X-RAY DIFFRACTION	99.62
2.12-2.23	0.1583	145	0.1567	2753	X-RAY DIFFRACTION	99.55
2.23-2.37	0.1477	152	0.159	2733	X-RAY DIFFRACTION	99.21
2.37-2.56	0.1799	143	0.1652	2744	X-RAY DIFFRACTION	99.14
2.56-2.81	0.1847	135	0.1781	2744	X-RAY DIFFRACTION	98.56
2.81-3.22	0.1712	135	0.1753	2750	X-RAY DIFFRACTION	98.3
3.22-4.06	0.162	151	0.1517	2784	X-RAY DIFFRACTION	98.72
4.06-39.78	0.1685	152	0.1468	2809	X-RAY DIFFRACTION	97.69

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	1.4257623966	-1.24041100918	-0.347724120519	3.44442271694	0.841350598657	1.27715424546	0.0903470255173	0.0746935386656	0.0856467665454	-0.280547863978	-0.0545733693763	-0.319119474344	-0.064442058373	0.191966017396	-0.0365916366222	0.115800547904	-0.00425705936421	0.0215035302245	0.145569803041	0.018575066096	0.127028586102	12.8068661141	3.79399276861	-34.838855844
2	1.51623563067	-0.311963856354	-1.16178789591	1.65808046841	0.505853890145	1.76048137093	0.0297134001875	-0.246399430649	0.141662040462	0.167932501596	0.0110621623388	-0.255026391293	-0.0792314744133	0.300595596538	-0.01403569838	0.181261566042	-0.0298152489003	-0.0335272414996	0.142222170201	-0.0120620208125	0.187300570237	13.4985914886	15.5289000445	-14.0951786145
3	0.78133935105	-0.329876277317	0.879525148682	0.911045615658	-0.988553329755	2.3559781756	0.00358709715794	-0.0203324769022	0.0285645886311	0.0630507059445	-0.0495667169131	-0.0739901267186	-0.0334976252353	0.0728984197215	0.0539598599254	0.108405792669	-0.0104280376061	0.00281610491549	0.0930166273071	-0.00307343035898	0.112775581315	7.8613241055	5.90130128058	-16.2616331724
4	4.456561811	-0.449822114245	0.723741908158	1.28584701292	-0.107063544893	1.99385358172	-0.0389765287722	-0.300624830646	-0.0293365737324	0.218947713317	-0.0271384660813	-0.0246619639222	-0.079459685678	0.054203252731	0.067115777164	0.187564482649	-0.0083650878676	0.00508893188363	0.114730333488	0.0058798732117	0.0966834235911	6.66127373645	-2.53206339686	-0.238926038423
5	2.21054167842	0.530947641606	1.25714564824	1.52323824643	0.332667989088	3.00466671144	-0.00348002594724	-0.16687032196	0.0056118188443	0.271592092298	-0.0573982098526	0.0168292827619	-0.0504509972598	-0.181325712444	0.0845534700433	0.141644330705	0.0091294370248	0.0146715198294	0.0936085384937	-0.0200300823978	0.110642360942	-1.70098560262	8.7831335458	-6.40532311285
6	3.93742717979	-1.45567124603	1.04995809358	1.64261853217	-0.193948893839	1.53379220069	0.0311088899252	-0.0988848753207	-0.0440348875276	0.115614562412	-0.00804387983767	-0.0111787039677	0.136948055063	0.00464459755868	-0.0421292006702	0.124608192854	-0.0174533430957	0.0125214984343	0.0907300292408	0.00356968911818	0.0886395522893	2.36664259969	-6.41066981844	-9.84311366021
7	3.20622607114	-1.85995513561	-0.279791039183	5.43976117011	-0.515094797835	1.84992238312	-0.0785561603159	-0.0870071325302	-0.107454060985	0.143990219403	0.0688121449623	-0.239247868706	0.190012114785	0.0567750313821	-0.00934901019121	0.127433609571	-0.00438597687207	-0.0023504964261	0.079128717003	-0.000695940954675	0.0934921835653	9.69430834564	-13.8490191789	-16.9937956038
8	1.06015423015	-0.581841359925	0.114034512573	0.885553703364	-0.0886791122382	1.06493114601	-0.00724936048329	0.0211726211715	-0.00997037693533	0.0266777865226	-0.0141303641006	0.031595384262	0.06904359122	-0.0619851857842	0.021963438259	0.105222114911	-0.0228825338383	0.00647760795991	0.0774872701391	-0.00474646115643	0.0894288885413	2.13134499444	-4.28869251363	-24.3174194503
9	3.25206471765	-0.205548359576	-0.476072551545	4.11811151374	-0.620002921289	2.9436777718	-0.0257345599789	-0.043249059812	-0.17745402586	0.316800848021	0.0230886376527	-0.412039320244	0.293642924238	0.540122375767	-0.0807444888393	0.134690810034	0.035225818976	-0.03282611508	0.163196138262	-0.00407970498492	0.157148173325	20.0807065726	-16.1642364768	-18.6043107933
10	5.24214015005	-1.98457251505	1.2949328778	1.66942304216	-0.4618166829	2.22882834873	0.107596917803	0.104048260079	-0.19022714719	-0.0658496445423	-0.0217989358446	0.0137076480328	0.163455185889	0.0909465122906	-0.0861720159293	0.141416091443	-0.0276858057554	0.00894583797363	0.0873095981231	-0.0239777286944	0.11235289578	5.32900193074	-9.61833658508	-34.8580048887
11	3.85639711957	-0.280310276832	0.476863325712	1.55825143201	-0.141165785093	1.58357615204	-0.0283771743932	0.0820045030655	0.0148126367781	-0.0838149449127	0.0206292316916	0.0814607789906	-0.0249989482845	-0.142728035785	0.0141799778847	0.0814350724763	-0.00259850907747	-0.000594978082742	0.0620663101654	-0.00146561432916	0.0466745922995	-0.760691094267	2.60141566284	-31.7061709081
12	3.95141040492	-0.147816321098	1.57497210696	2.65918693854	-0.423656442609	2.0333414986	-0.0352151029932	-0.0100702454162	0.039323039998	0.187517460366	-0.0177020700915	-0.169876317734	-0.0660584518316	0.335239955469	0.0487901634805	0.164621754823	-0.0292323476536	-0.00711137012623	0.208714099454	-0.00312076671919	0.190452408818	25.1378656919	2.98535612952	-14.7522743006

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 250 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 251 through 268 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 269 through 301 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 302 through 335 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 336 through 355 )

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