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- PDB-7s0h: Crystal structure of Penicillium verruculosum copalyl diphosphate... -

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Basic information

Entry
Database: PDB / ID: 7s0h
TitleCrystal structure of Penicillium verruculosum copalyl diphosphate synthase (PvCPS) alpha prenyltransferase domain variant, S723Y
ComponentsTerpene synthase
KeywordsTRANSFERASE / 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 / isoprenoid biosynthetic process / isomerase activity / transferase activity / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Copalyl diphosphate synthase
Similarity search - Component
Biological speciesTalaromyces verruculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsRonnebaum, T.A. / Christianson, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
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)F32GM137461 United States
CitationJournal: 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
DepositionAug 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: 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 1.2Nov 10, 2021Group: 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 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terpene synthase
B: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)69,9582
Polymers69,9582
Non-polymers00
Water0
1
A: Terpene synthase
B: Terpene synthase

A: Terpene synthase
B: Terpene synthase

A: Terpene synthase
B: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)209,8756
Polymers209,8756
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area22110 Å2
ΔGint-130 kcal/mol
Surface area67040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.534, 188.534, 56.442
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
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

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Components

#1: Protein Terpene synthase /


Mass: 34979.109 Da / Num. of mol.: 2 / Fragment: Prenyltransferase alpha domain, residues 659-963 / Mutation: S723Y
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 detailsThe 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: MSPMDLQESAAALVRQLGERVEDRRGFGFMSPAIYDTAWVSMISKTIDDQKTWLFAECFQYILSHQLEDGGWAMYASEID AILNTSASLLSLKRHLSNPYQITSITQEDLSARINRAQNALQKLLNEWNVDSTLHVGFEILVPALLRYLEDEGIAFAFSG RERLLEIEKQKLSKFKAQYLYLPIKVTALHSLEAFIGAIEFDKVSHHKVSGAFMASPSSTAAYMMHATQWDDECEDYLRH VIAHASGKGSGGVPSAFPSTIFESVWPLSTLLKVGYDLNSAPFIEKIRSYLHDAYIAEKGILGFTPFVGADADDTATTIL VLNLLNQPVSVDAMLKEFEEEHHFKTYSQERNPSFSANCNVLLALLYSQEPSLYSAQIEKAIRFLYKQFTDSEMDVRDKW NLSPYYSWMLMTQAITRLTTLQKTSKLSTLRDDSISKGLISLLFRIASTVVKDQKPGGSWGTRASKEETAYAVLILTYAF YLDEVTESLRHDIKIAIENGCSFLSERTMQSDSEWLWVEKVTYKSEVLSEAYILAALKRAADLPDENAEAAPVINGISTN GFEHTDRINGKLKVNGTNGTNGSHETNGINGTHEIEQINGVNGTNGHSDVPHDTNGWVEEPTAINETNGHYVNGTNHETP LTNGISNGDSVSVHTDHSDSYYQRSDWTADEEQILLGPFDYLESLPGKNMRSQLIQSFNTWLKVPTESLDVIIKVISMLH TAYLLIDDIQDQSILRRGQPVAHSIFGTAQAMNSGNYVYFLALREVQKLQNPKAISIYVDSLIDLHRGQGMELFWRDSLM CPTEEQYLDMVANKTGGLFCLAIQLMQAEATIQVDFIPLVRLLGIIFQICDDYLNLKSTAYTDNKGLCEDLTEGKFSFPI IHSIRSNPGNRQLINILKQKPREDDIKRYALSYMESTNSFEYTRGVVRKLKTEAIDTIQGLEKHGLEENIGIRKILARMS LEL

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6 2.5% tacsimate pH 5.0 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.15→81.64 Å / Num. obs: 143593 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 37.62 Å2 / CC1/2: 0.947 / Net I/σ(I): 5.3
Reflection shellResolution: 3.15→3.263 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 20131 / CC1/2: 0.509

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V0K

6v0k


Resolution: 3.15→81.64 Å / SU ML: 0.407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 3872 10.01 %
Rwork0.1862 34826 -
obs0.191 38698 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.41 Å2
Refinement stepCycle: LAST / Resolution: 3.15→81.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 0 0 4770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124871
X-RAY DIFFRACTIONf_angle_d1.36886610
X-RAY DIFFRACTIONf_chiral_restr0.0541762
X-RAY DIFFRACTIONf_plane_restr0.0082849
X-RAY DIFFRACTIONf_dihedral_angle_d8.9459665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.190.37221370.31831206X-RAY DIFFRACTION98.9
3.19-3.230.33921410.31561256X-RAY DIFFRACTION99.01
3.23-3.270.3321280.28951196X-RAY DIFFRACTION98.15
3.27-3.320.32211410.27521295X-RAY DIFFRACTION98.9
3.32-3.360.30061360.26751219X-RAY DIFFRACTION99.93
3.36-3.410.31341360.24641220X-RAY DIFFRACTION99.93
3.41-3.470.26761400.24821266X-RAY DIFFRACTION100
3.47-3.520.33571330.22721278X-RAY DIFFRACTION100
3.52-3.580.27661360.23091220X-RAY DIFFRACTION100
3.58-3.650.29021400.23241248X-RAY DIFFRACTION99.93
3.65-3.720.25621460.20341274X-RAY DIFFRACTION99.93
3.72-3.80.26881340.20521247X-RAY DIFFRACTION100
3.8-3.880.27161320.19471216X-RAY DIFFRACTION99.93
3.88-3.970.26631340.19591250X-RAY DIFFRACTION99.93
3.97-4.070.20271450.17481256X-RAY DIFFRACTION99.93
4.07-4.180.19861360.16721242X-RAY DIFFRACTION99.93
4.18-4.30.20621460.15471262X-RAY DIFFRACTION99.86
4.3-4.440.21241380.14961215X-RAY DIFFRACTION99.05
4.44-4.60.1581360.13021259X-RAY DIFFRACTION99.71
4.6-4.780.1791400.12381252X-RAY DIFFRACTION99.43
4.78-50.20261320.14341218X-RAY DIFFRACTION100
5-5.260.22541480.15951270X-RAY DIFFRACTION100
5.27-5.590.22381430.17581245X-RAY DIFFRACTION100
5.6-6.020.23551380.17731233X-RAY DIFFRACTION100
6.03-6.630.22291280.17941254X-RAY DIFFRACTION100
6.63-7.590.17011480.14841245X-RAY DIFFRACTION99.93
7.59-9.550.12631370.10021251X-RAY DIFFRACTION99.14
9.57-81.640.13911430.12291233X-RAY DIFFRACTION98.78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.200288819791.656012973260.4598735353610.6373889667950.156353768176-0.00130934238698-0.8452448067020.848613883764-0.851197337545-0.994139129666-0.812370077626-0.1246516693912.01259991947-0.8266604212680.3645257291860.696409395476-0.399044326333-0.09531593739640.7835688897650.03011962382520.649783673583-85.263615077841.1277465322-2.08612912671
24.82490918582-2.17252095481-0.7874936000863.83107598345-2.758062035993.213414404410.0017609410956-1.04471027223-0.6939822030410.525289774452-0.0430018411481-0.3392512921270.8703380078862.4938374550.01468521093950.5342798074070.0961558500372-0.1507482164360.7289017690320.1314964893120.576967229956-98.413119404739.152982541.0925317896
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 858 - 870

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11chain 'A' and (resid 858 through 870 )AA199 - 211
22chain 'B' and (resid 858 through 870 )BB200 - 212

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