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- PDB-7s0m: Crystal structure of Penicillium verruculosum copalyl diphosphate... -

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Basic information

Entry
Database: PDB / ID: 7s0m
TitleCrystal structure of Penicillium verruculosum copalyl diphosphate synthase (PvCPS) alpha prenyltransferase domain variant, S723T, bound with non-productive isopentenyl diphosphate
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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Copalyl diphosphate synthase
Similarity search - Component
Biological speciesTalaromyces verruculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)GM137461 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

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Assembly

Deposited unit
A: Terpene synthase
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3264
Polymers69,8342
Non-polymers4922
Water9,602533
1
A: Terpene synthase
B: Terpene synthase
hetero molecules

A: Terpene synthase
B: Terpene synthase
hetero molecules

A: Terpene synthase
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,97912
Polymers209,5026
Non-polymers1,4776
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area25070 Å2
ΔGint-137 kcal/mol
Surface area66840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.801, 189.801, 56.483
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
Components on special symmetry positions
IDModelComponents
11A-1262-

HOH

21B-1205-

HOH

31B-1273-

HOH

41B-1322-

HOH

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Components

#1: Protein Terpene synthase /


Mass: 34917.039 Da / Num. of mol.: 2 / Fragment: Prenyltransferase alpha domain, residues 659-963 / Mutation: S723T
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
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 TATLLIDDIQDQSILRRGQPVAHSIFGTAQAMNSGNYVYFLALREVQKLQNPKAISIYVDSLIDLHRGQGMELFWRDSLM 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: 4.21 Å3/Da / Density % sol: 70.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6 0.015 M sodium citrate tribasic dihydrate 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-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→62.13 Å / Num. obs: 762371 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 26.55 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.96
Reflection shellResolution: 2→2.071 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 78736 / CC1/2: 0.505

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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: 2→62.13 Å / SU ML: 0.2571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1949 3923 2.55 %
Rwork0.1755 149851 -
obs0.176 153774 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.75 Å2
Refinement stepCycle: LAST / Resolution: 2→62.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4837 0 28 533 5398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714984
X-RAY DIFFRACTIONf_angle_d0.80986759
X-RAY DIFFRACTIONf_chiral_restr0.0452770
X-RAY DIFFRACTIONf_plane_restr0.0068868
X-RAY DIFFRACTIONf_dihedral_angle_d10.6211680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.3471360.32635401X-RAY DIFFRACTION99.91
2.02-2.050.35691340.30985263X-RAY DIFFRACTION100
2.05-2.080.33321480.30055364X-RAY DIFFRACTION99.91
2.08-2.110.32691380.28075359X-RAY DIFFRACTION99.98
2.11-2.140.2841440.27195344X-RAY DIFFRACTION99.96
2.14-2.170.28681440.2535384X-RAY DIFFRACTION99.98
2.17-2.20.26421340.24885359X-RAY DIFFRACTION100
2.2-2.240.24931440.23585325X-RAY DIFFRACTION100
2.24-2.280.27371440.22545369X-RAY DIFFRACTION99.95
2.28-2.320.24581330.22015313X-RAY DIFFRACTION99.96
2.32-2.360.24811340.21755417X-RAY DIFFRACTION99.84
2.36-2.410.24851440.21175268X-RAY DIFFRACTION99.87
2.41-2.460.18321400.19945415X-RAY DIFFRACTION99.96
2.46-2.520.20551460.18695310X-RAY DIFFRACTION99.98
2.52-2.580.16711360.17025343X-RAY DIFFRACTION100
2.58-2.650.19561440.17325334X-RAY DIFFRACTION100
2.65-2.730.2061360.17315368X-RAY DIFFRACTION100
2.73-2.820.16571360.16475402X-RAY DIFFRACTION100
2.82-2.920.21491400.16315322X-RAY DIFFRACTION99.98
2.92-3.040.15251400.16185329X-RAY DIFFRACTION100
3.04-3.170.19221400.17745390X-RAY DIFFRACTION100
3.17-3.340.15721400.1595361X-RAY DIFFRACTION100
3.34-3.550.13221350.13985371X-RAY DIFFRACTION99.96
3.55-3.820.15781440.12875305X-RAY DIFFRACTION100
3.83-4.210.18961420.13835362X-RAY DIFFRACTION100
4.21-4.820.13951460.12555359X-RAY DIFFRACTION99.96
4.82-6.070.19611420.16295351X-RAY DIFFRACTION100
6.07-62.130.16751390.15095363X-RAY DIFFRACTION99.71

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