PDB-8su2: F96H epi-Isozizaene Synthase: complex with 3 Mg2+ and risedronate

ID or keywords:

Entry

Database: PDB / ID: 8su2

Title

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

Components

Epi-isozizaene synthase

Keywords

LYASE /

Terpene /

Terpenoid /

Isoprenoid / Terpene cyclase /

terpene synthase

Function / homology

epi-isozizaene synthase /

epi-isozizaene synthase activity / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily /

metal ion binding / Chem-RIS /

Epi-isozizaene synthase

Function and homology information

Biological species

Streptomyces coelicolor A3

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.33 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	8su2.cif.gz	176.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8su2.ent.gz	119.2 KB	Display	PDB format
PDBx/mmJSON format	8su2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/su/8su2 ftp://data.pdbj.org/pub/pdb/validation_reports/su/8su2	HTTPS FTP

-
Related structure data

Related structure data	8su0C 8su1C 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

-
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

44.3 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)	51.546, 46.841, 75.170
Angle α, β, γ (deg.)	90.000, 98.066, 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: 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

#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

-
Non-polymers , 5 types, 253 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate 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 / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate / Risedronic acid Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₁NO₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#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: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.06 Å³/Da / Density % sol: 40.17 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris (pH 6.5), 200 mM (NH4)2SO4, 30% (w/v) PEG 3350, 100 mM NaBr

-
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: 1.33→51.04 Å / Num. obs: 79951 / % possible obs: 98 % / Redundancy: 3.2 % / B_iso Wilson estimate: 12.72 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.049 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.33→1.35 Å / R_merge(I) obs: 0.292 / Mean I/σ(I) obs: 3 / Num. unique obs: 3937 / CC_1/2: 0.894

-
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: 1.33→51.04 Å / SU ML: 0.0996 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.2741 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1724	3890	4.87 %
R_work	0.1603	76028	-
obs	0.1609	79918	97.88 %

Solvent computation

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

Displacement parameters

B_iso mean: 16.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.33→51.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2713	0	31	247	2991

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	2822
X-RAY DIFFRACTION	f_angle_d	1.0035	3856
X-RAY DIFFRACTION	f_chiral_restr	0.0783	406
X-RAY DIFFRACTION	f_plane_restr	0.0073	496
X-RAY DIFFRACTION	f_dihedral_angle_d	17.5931	985

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 (%)
1.33-1.35	0.2331	135	0.1947	2735	X-RAY DIFFRACTION	98.02
1.35-1.36	0.1738	145	0.1863	2716	X-RAY DIFFRACTION	98.66
1.36-1.38	0.1935	118	0.1766	2701	X-RAY DIFFRACTION	98.53
1.38-1.4	0.1759	141	0.1715	2693	X-RAY DIFFRACTION	98.1
1.4-1.42	0.2168	114	0.1677	2762	X-RAY DIFFRACTION	98.02
1.42-1.44	0.187	128	0.1645	2628	X-RAY DIFFRACTION	96.57
1.44-1.46	0.2026	143	0.1677	2530	X-RAY DIFFRACTION	91.64
1.46-1.49	0.1806	143	0.152	2742	X-RAY DIFFRACTION	99.79
1.49-1.51	0.1889	133	0.1577	2794	X-RAY DIFFRACTION	99.9
1.51-1.54	0.1688	120	0.1534	2749	X-RAY DIFFRACTION	99.58
1.54-1.57	0.1731	142	0.1533	2754	X-RAY DIFFRACTION	99.76
1.57-1.6	0.1695	124	0.1448	2768	X-RAY DIFFRACTION	99.66
1.6-1.64	0.1666	135	0.1421	2753	X-RAY DIFFRACTION	99.69
1.64-1.68	0.1721	137	0.1494	2778	X-RAY DIFFRACTION	99.35
1.68-1.72	0.1648	146	0.1461	2724	X-RAY DIFFRACTION	99.41
1.72-1.76	0.1696	161	0.1487	2731	X-RAY DIFFRACTION	99.01
1.76-1.82	0.151	149	0.1531	2707	X-RAY DIFFRACTION	98.96
1.82-1.87	0.1572	137	0.154	2758	X-RAY DIFFRACTION	98.4
1.87-1.94	0.1741	151	0.1556	2702	X-RAY DIFFRACTION	97.77
1.94-2.02	0.1798	128	0.1552	2677	X-RAY DIFFRACTION	96.72
2.02-2.11	0.1882	161	0.1518	2690	X-RAY DIFFRACTION	97.6
2.11-2.22	0.1665	162	0.1517	2677	X-RAY DIFFRACTION	97.56
2.22-2.36	0.1639	154	0.1579	2692	X-RAY DIFFRACTION	96.93
2.36-2.54	0.1708	140	0.1638	2675	X-RAY DIFFRACTION	96.87
2.54-2.8	0.1958	131	0.1673	2708	X-RAY DIFFRACTION	96.53
2.8-3.21	0.1511	140	0.1626	2681	X-RAY DIFFRACTION	95.85
3.21-4.04	0.1526	139	0.1584	2733	X-RAY DIFFRACTION	96.38
4.04-51.04	0.1883	133	0.175	2770	X-RAY DIFFRACTION	95.56

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	1.00012203655	-1.10765124827	-0.594471946258	2.66247203569	0.897259676861	1.32761012126	0.0569702824463	0.0195865379463	0.0654457090183	-0.147334023441	-0.018990122764	-0.168023649998	-0.0712797994281	0.146498292207	-0.0360291061293	0.111294002322	-0.010671083082	0.00652523931794	0.145258880123	0.0077884651859	0.1182781494	7.60924979281	2.601013796	2.49804657945
2	1.92902247074	-0.367540796787	-0.767780652658	1.50597973818	-0.0882082671487	1.54485695468	0.0660246304813	-0.243806671527	0.122576886651	0.126178668875	-0.00405729115052	-0.137221634614	-0.121485364659	0.203277877593	-0.0455977770227	0.180280184708	-0.0366980427705	-0.0124973964562	0.137372211194	-0.0243010712532	0.162452784192	8.01111623238	14.639227789	23.5015901554
3	1.30759618352	-0.63320161487	1.09776167681	1.35294422388	-1.17048408562	2.90472621962	-0.0129348490054	-0.0267644000905	0.0255474658689	0.061678444553	-0.0159868190699	-0.0317440757943	-0.0570191133628	0.0253184379958	0.0407678260137	0.0970181921618	-0.0113082134608	0.00519463294282	0.0788906271826	-0.00917319721314	0.0930201108485	2.53990935027	4.98602623559	21.0794718833
4	6.06470053862	-0.544125655675	0.793031713074	1.31309855774	0.0308018311587	1.97276787218	-0.0670005945628	-0.401376715971	-0.0566690675658	0.185383541232	-0.0121112017061	-4.87827331267E-5	-0.0524792740226	0.0507386317175	0.0838113918378	0.190102243737	-0.00372070569637	0.00213255707708	0.132414306647	0.00489609316606	0.102068703398	1.33174474176	-3.29702573875	37.1543903182
5	2.10238066411	0.48309090071	1.67397595879	1.24733348603	0.439089267182	3.27559154799	-0.0145144618108	-0.153733696071	-0.0181799457291	0.176413859937	-0.0241495005108	0.00225962302817	-0.0666462287595	-0.194906639855	0.058582657288	0.132779711951	0.0111449566341	0.0192520427743	0.107698294287	-0.0157524824842	0.115762076546	-7.00378241958	7.92153648214	30.8005807388
6	1.52485533863	-0.668369354975	-0.251199793413	1.35920365114	0.452090050678	1.17355790208	-0.0320018990034	-0.068026396143	-0.111334666687	0.112017721471	0.0330003779536	-0.052583868274	0.180061473955	0.0355728111405	-0.000237752035512	0.138361556485	-0.012766084231	0.00762494884701	0.0845941626027	0.0120723270779	0.109378808483	-0.227598566799	-9.99793403064	24.7212341864
7	2.0666873466	-0.674535359894	0.323684522305	0.995568754922	-0.0721650667205	1.06173400211	-0.0293280004503	0.0240238296834	-0.0743635331134	0.0184445318794	0.000633802836523	0.0668840993715	0.0531273042473	-0.0680857952849	0.0246158357516	0.100023307995	-0.0205965739568	0.00861176171824	0.0791073089299	-6.45946329778E-5	0.0868075607049	-3.18270565843	-5.43918816793	13.0192227733
8	3.38947547742	-0.534508521565	-0.434578078367	4.62798981807	-0.0619457917969	3.38894822571	-0.0145406202756	0.0429584033208	-0.175468481442	0.237834134812	0.00311604578241	-0.3141507332	0.306923473247	0.42763419449	-0.0181387282435	0.142650117449	0.0324901094698	-0.00900771116498	0.160404808373	-0.00295208592203	0.174066620483	14.9776541414	-16.8788061982	18.8873494397
9	6.73439878136	-2.33059059452	1.40314917417	1.89575335182	-0.387111231733	2.14678636647	0.0423475993952	0.207747038151	-0.153300476784	-0.0560917196599	-0.0201894442314	0.00940573706481	0.130123102521	0.142242811604	-0.0436271112237	0.138269817523	-0.0180203939563	0.0116834629056	0.0778453202384	-0.0161812894297	0.106331519147	-0.0467236886907	-10.6138930423	2.57531407986
10	5.14152559015	-0.317608604171	0.741927877687	1.37033925222	-0.0679885391512	1.49103560127	-0.0231337953688	0.153847498893	-0.00174636293951	-0.0781677106748	0.032819339713	0.123830255366	-0.0450420263866	-0.111338909594	-0.00667872678442	0.0941374961117	-0.00218032731478	-0.00179555557353	0.0696849774419	0.000146865697888	0.064234617857	-6.11874819607	1.53942433612	5.65319778062
11	4.84981691975	-0.0174135774567	1.86407318149	3.26337921559	-0.575797104185	2.72301018911	-0.0369681903022	0.0426080495627	0.00522444252455	0.126987038001	-0.0200367939855	-0.218224178752	-0.0524722006659	0.388024781097	0.0486148512582	0.096219746506	-0.0219903185563	-0.000908803175551	0.129834796525	0.000473880108877	0.122903158545	19.8107154861	2.16457826099	22.6624626327

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 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 )

-
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 , 5 types, 253 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 , 5 types, 253 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 , 5 types, 253 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