PDB-7s0l: Crystal structure of Penicillium verruculosum copalyl diphosphate...

ID or keywords:

Entry

Database: PDB / ID: 7s0l

Title

Crystal structure of Penicillium verruculosum copalyl diphosphate synthase (PvCPS) alpha prenyltransferase domain variant, S723F

Components

Terpene synthase

Keywords

TRANSFERASE / Prenyltransferase / Isoprenoid Synthase / GGPP synthase / Bifunctional Terpene Synthase / Assembly-line synthase

Function / homology

Function and homology information

copalyl diphosphate synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / prenyltransferase activity / isoprenoid biosynthetic process / isomerase activity / metal ion binding
Similarity search - Function

Biological species

Talaromyces verruculosus (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Ronnebaum, T.A. / Christianson, D.W.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM56838	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM137461	United States

Citation

Journal: Biochemistry / Year: 2021
Title: Engineering the Prenyltransferase Domain of a Bifunctional Assembly-Line Terpene Synthase.
Authors: Ronnebaum, T.A. / Eaton, S.A. / Brackhahn, E.A.E. / Christianson, D.W.

History

Deposition	Aug 30, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 20, 2021	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 10, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7s0l.cif.gz	299.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7s0l.ent.gz	203.3 KB	Display	PDB format
PDBx/mmJSON format	7s0l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7s0l_validation.pdf.gz	418.9 KB	Display	wwPDB validaton report
Full document	7s0l_full_validation.pdf.gz	422.5 KB	Display
Data in XML	7s0l_validation.xml.gz	20.9 KB	Display
Data in CIF	7s0l_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s0/7s0l ftp://data.pdbj.org/pub/pdb/validation_reports/s0/7s0l	HTTPS FTP

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Related structure data

Related structure data	7s09C 7s0aC 7s0hC 7s0mC 6v0kS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7s0h-1 7s09-1 5ero-1 2q80-d 7s0m-1 6v0k-1 7s0a-1 5cdo-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (7) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

A: Terpene synthase

B: Terpene synthase

69.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Terpene synthase

B: Terpene synthase

A: Terpene synthase

B: Terpene synthase

A: Terpene synthase

B: Terpene synthase

defined by author&software
Evidence: gel filtration
210 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	189.280, 189.280, 56.373
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321
Space group name Hall	P32"
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x-y,-y,-z #5: -x,-x+y,-z #6: y,x,-z

#1: Protein	Terpene synthase Mass: 34963.109 Da / Num. of mol.: 2 / Fragment: Prenyltransferase alpha domain, residues 659-963 / Mutation: S723F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces verruculosus (fungus) / Gene: PvCPS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A348FUE1
Sequence details	The authors state that the full-length enzyme is a chimera, consisting of 963 residues. However, ...The authors state that the full-length enzyme is a chimera, consisting of 963 residues. However, the provided crystal structure was generated from limited proteolysis experiments and only the prenyltransferase alpha domain of the chimera was crystallized. The sequence of the full-length enzyme is: MSPMDLQESAAALVRQLGERVEDRRGFGFMSPAIYDTAWVSMISKTIDDQKTWLFAECFQYILSHQLEDG GWAMYASEIDAILNTSASLLSLKRHLSNPYQITSITQEDLSARINRAQNALQKLLNEWNVDSTLHVGFEI LVPALLRYLEDEGIAFAFSGRERLLEIEKQKLSKFKAQYLYLPIKVTALHSLEAFIGAIEFDKVSHHKVS GAFMASPSSTAAYMMHATQWDDECEDYLRHVIAHASGKGSGGVPSAFPSTIFESVWPLSTLLKVGYDLNS APFIEKIRSYLHDAYIAEKGILGFTPFVGADADDTATTILVLNLLNQPVSVDAMLKEFEEEHHFKTYSQE RNPSFSANCNVLLALLYSQEPSLYSAQIEKAIRFLYKQFTDSEMDVRDKWNLSPYYSWMLMTQAITRLTT LQKTSKLSTLRDDSISKGLISLLFRIASTVVKDQKPGGSWGTRASKEETAYAVLILTYAFYLDEVTESLR HDIKIAIENGCSFLSERTMQSDSEWLWVEKVTYKSEVLSEAYILAALKRAADLPDENAEAAPVINGISTN GFEHTDRINGKLKVNGTNGTNGSHETNGINGTHEIEQINGVNGTNGHSDVPHDTNGWVEEPTAINETNGH YVNGTNHETPLTNGISNGDSVSVHTDHSDSYYQRSDWTADEEQILLGPFDYLESLPGKNMRSQLIQSFNT WLKVPTESLDVIIKVISMLHTAFLLIDDIQDQSILRRGQPVAHSIFGTAQAMNSGNYVYFLALREVQKLQ NPKAISIYVDSLIDLHRGQGMELFWRDSLMCPTEEQYLDMVANKTGGLFCLAIQLMQAEATIQVDFIPLV RLLGIIFQICDDYLNLKSTAYTDNKGLCEDLTEGKFSFPIIHSIRSNPGNRQLINILKQKPREDDIKRYA LSYMESTNSFEYTRGVVRKLKTEAIDTIQGLEKHGLEENIGIRKILARMSLEL

#1: Protein

Terpene synthase

Mass: 34963.109 Da / Num. of mol.: 2 / Fragment: Prenyltransferase alpha domain, residues 659-963 / Mutation: S723F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Talaromyces verruculosus (fungus) / Gene: PvCPS / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A348FUE1

Sequence details

The authors state that the full-length enzyme is a chimera, consisting of 963 residues. However, ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.17 Å³/Da / Density % sol: 70.5 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate pH 5.6 0.01 M citric acid pH 3.5 2.5% tacsimate pH 5.0 18% 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: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 17, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.65→94.64 Å / Num. obs: 323109 / % possible obs: 99.9 % / Redundancy: 9.5 % / B_iso Wilson estimate: 28.2 Å² / CC_1/2: 0.986 / Net I/σ(I): 7.6
Reflection shell	Resolution: 2.65→2.75 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 33846 / CC_1/2: 0.521

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6V0K

6v0k

Resolution: 2.65→94.64 Å / SU ML: 0.3749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5504 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2294	3850	5.88 %
R_work	0.1896	61678	-
obs	0.1919	65528	99.75 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→94.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4809	0	0	0	4809

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	4921
X-RAY DIFFRACTION	f_angle_d	0.8895	6665
X-RAY DIFFRACTION	f_chiral_restr	0.0455	763
X-RAY DIFFRACTION	f_plane_restr	0.0049	854
X-RAY DIFFRACTION	f_dihedral_angle_d	4.5219	4144

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 (%)
2.65-2.68	0.3345	152	0.2987	2319	X-RAY DIFFRACTION	99.64
2.68-2.72	0.3312	136	0.2959	2229	X-RAY DIFFRACTION	99.54
2.72-2.76	0.3177	138	0.2914	2280	X-RAY DIFFRACTION	99.71
2.76-2.8	0.3535	143	0.3007	2328	X-RAY DIFFRACTION	99.68
2.8-2.84	0.3564	141	0.299	2242	X-RAY DIFFRACTION	99.62
2.84-2.88	0.3914	136	0.2909	2264	X-RAY DIFFRACTION	99.46
2.88-2.93	0.3153	150	0.2727	2301	X-RAY DIFFRACTION	100
2.93-2.98	0.3023	148	0.2667	2339	X-RAY DIFFRACTION	100
2.98-3.03	0.2622	140	0.2465	2269	X-RAY DIFFRACTION	100
3.03-3.09	0.3087	144	0.2453	2305	X-RAY DIFFRACTION	100
3.09-3.15	0.3308	142	0.2405	2275	X-RAY DIFFRACTION	100
3.15-3.22	0.3017	142	0.2528	2239	X-RAY DIFFRACTION	100
3.22-3.3	0.284	136	0.2203	2339	X-RAY DIFFRACTION	99.92
3.3-3.38	0.289	141	0.2166	2263	X-RAY DIFFRACTION	99.92
3.38-3.47	0.2512	146	0.1953	2273	X-RAY DIFFRACTION	99.83
3.47-3.57	0.2154	146	0.1662	2318	X-RAY DIFFRACTION	99.88
3.57-3.69	0.2139	143	0.1695	2262	X-RAY DIFFRACTION	99.83
3.69-3.82	0.1869	152	0.1487	2280	X-RAY DIFFRACTION	99.79
3.82-3.97	0.1776	144	0.148	2268	X-RAY DIFFRACTION	99.46
3.97-4.16	0.1758	142	0.1398	2269	X-RAY DIFFRACTION	99.42
4.16-4.37	0.1502	138	0.1283	2304	X-RAY DIFFRACTION	99.07
4.37-4.65	0.1405	145	0.1111	2269	X-RAY DIFFRACTION	99.92
4.65-5.01	0.1434	148	0.1227	2280	X-RAY DIFFRACTION	100
5.01-5.51	0.212	141	0.1588	2291	X-RAY DIFFRACTION	100
5.51-6.31	0.1888	146	0.1545	2305	X-RAY DIFFRACTION	99.96
6.31-7.95	0.1624	150	0.1606	2272	X-RAY DIFFRACTION	99.34
7.95-94.64	0.174	120	0.1398	2295	X-RAY DIFFRACTION	99.38

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	0.753553046166	0.498692359592	0.608500207118	1.80968298076	0.49261302128	0.71050800457	-0.0469652864037	0.0830990202681	-0.0846938842622	-0.0270612058803	0.100970517002	0.00213204646892	0.0935189232001	-0.00295198788256	-0.0551931867923	0.148566223448	-0.0271558964917	0.00271313392509	0.163309233271	-0.0266854501936	0.15173719783	-28.0032067084	93.9583678618	37.4533817661
2	3.02818895647	0.283835016421	0.548392263921	0.401885182134	-0.139013872898	0.111624912202	0.0235260395565	0.387733758261	-0.0316963806448	-0.0884452023931	0.00288802544652	0.0249929346914	-0.00339656761011	0.0396585824201	-0.0238129677701	0.199984257117	0.00904703999066	0.00239178012647	0.224762412373	-0.0232781349405	0.135463480301	-11.5547631715	80.8838302269	31.5986535104
3	2.10324432825	-1.99665545582	-2.41618262333	4.06030963967	-0.43729404684	7.6199660446	0.0999457142335	0.197324596053	-0.244013697448	-0.904340265604	-0.108926039458	0.217643342603	0.584326498772	-0.251461947492	0.0587804105647	0.265686684839	-0.0898416735325	0.0122397535038	0.211153218715	0.0883439441697	0.355886098647	-12.2914320595	72.560046441	44.3763099198
4	2.28965143536	-0.450344566878	-0.767022951857	0.0697128628236	0.149030406519	0.286526898236	0.409588494282	-0.0874518149401	0.390281113383	0.247699528315	-0.0700336016131	0.0983530590109	0.0644497826282	0.0112684153753	-0.306318703155	0.216137517963	-0.0728998178215	0.0763748124759	0.316347017762	-0.00747982436828	0.243684084985	-27.3805714862	86.7873389466	67.5988545897
5	4.84708190604	5.4047655695	-4.74850161299	6.21941187801	-4.97007399231	5.44241482365	0.305679033292	-0.417854754435	0.188720139888	0.186289872501	-0.348708502262	0.25420506056	-0.249253309857	0.186459469706	0.097745873662	0.130135123661	0.000528322282244	0.0260857511652	0.223572859638	-0.00552825377884	0.199423149664	-25.6391811288	87.0804742415	60.1682301837
6	4.64648669743	1.26718562282	1.16394797952	0.874630816269	0.336964899213	1.41655872564	0.0909155704322	-0.0878012351055	0.0236910124955	0.0876166607254	-0.0465756371147	-0.100161125866	0.163692022274	-0.105092045768	-0.0344116976697	0.139022389948	-0.0052510694901	0.0194831494529	0.107404343568	-0.0165558238504	0.124067801414	-20.4232982542	87.8730723736	55.1102186103
7	4.55483886988	4.55853663534	-0.752850338883	4.83188747828	-1.2953188414	1.34611151404	0.022088827432	0.252118162443	0.138180616023	0.648580572179	0.466257349749	0.1117285983	0.193076093945	0.295653115768	-0.224299649568	0.209176400782	0.0122440969271	0.0367802424132	0.175233391702	-0.0232252531413	0.188643858871	-30.6130730319	98.8251066331	51.0358241044
8	3.25421051407	3.0293770792	-0.569234025615	4.15480539357	-2.93681365146	4.83149962367	-0.0603772285201	0.120290251025	-0.218742574793	0.280116972324	-0.267431245368	-0.435393619115	-0.0137666513377	-0.282037172035	0.215093855976	0.232638351048	0.0216427874459	0.0238341485742	0.278711603295	-0.0756173184879	0.192278658312	-32.2468671773	109.112698731	56.7437238481
9	4.12172819661	-1.65713519407	-2.86026043337	8.43052667036	-1.07876886429	8.284027566	0.105107495627	0.194983359204	0.216596494151	-0.167670319244	-0.0232351357925	0.108417829457	-0.180037011246	-0.187443319169	-0.116287492712	0.122060763986	-0.0207414166535	0.00143118988313	0.176081264293	-0.0378774769677	0.11665839823	-41.1907983762	87.658845003	62.8645173094
10	7.65740485284	4.66181600155	0.22194813607	4.18745997448	-0.418651326388	1.01796915156	-0.293580609672	0.0108323268537	-0.230766599588	-0.257753704812	0.188201654566	-0.14895760205	-0.124139629509	0.260416734364	0.0875054648547	0.393161253403	-0.00955679980936	0.0622849350638	0.103992384197	-0.0423097321556	0.196577065975	-31.0053939534	103.259677937	67.2890412457
11	5.61020785355	-0.869950683537	-0.765756524289	3.30757348786	-0.583032908598	4.02544686735	0.172374381868	-0.557180759332	-0.0983127995081	0.481322123798	-0.213377250331	-0.29849411563	0.224490259358	0.211955175463	0.0545581531907	0.293274802398	-0.0815806341656	-0.0510405286495	0.208543702759	8.43206872181E-5	0.206181851402	-18.8401177896	115.577836196	63.4334074489
12	8.16190897176	7.33690046175	-2.30132456357	7.39853678379	-2.25596902897	1.96640421137	0.419638962605	-0.177664305848	0.0703640109146	0.879928542192	-0.2981978397	0.645355677208	-0.450747940164	-0.350872867805	-0.169581959728	0.341870322564	0.0730692153014	0.0669478225623	0.246537801339	0.0108727516677	0.251501844817	-38.993813955	106.525900049	73.4342073091
13	3.78569433284	5.05175977959	1.4003943347	8.95903838941	-0.287640788891	8.13449741389	0.299005777056	-0.123395636538	0.195462981804	0.772428923764	-0.189686814095	-0.037500298208	-0.420549413994	0.0599347021669	-0.0599263276965	0.38127240577	-0.0278799642196	0.0488068088828	0.286759833746	0.0277116370364	0.191015974935	-37.5773563662	95.7977130513	77.3511493899

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 660 through 769 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 770 through 960 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 660 through 675 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 676 through 705 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 706 through 730 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 731 through 773 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 774 through 798 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 799 through 815 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 816 through 836 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 837 through 857 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 858 through 918 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 919 through 943 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 944 through 963 )

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+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