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- PDB-8v3k: F95S-F198S epi-Isozizaene Synthase: complex with 3 Mg2+, inorgani... -

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Basic information

Entry
Database: PDB / ID: 8v3k
TitleF95S-F198S epi-Isozizaene Synthase: complex with 3 Mg2+, inorganic pyrophosphate, and benzyl triethyl ammonium cation
ComponentsEpi-isozizaene synthase
KeywordsLYASE / Terpene / Terpenoid / Isoprenoid / Cyclase
Function / homology
Function and homology information


epi-isozizaene synthase / epi-isozizaene synthase activity / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / : / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
N-benzyl-N,N-diethylethanaminium / DIPHOSPHATE / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsChristianson, D.W. / Eaton, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2024
Title: Structure-Based Engineering of a Sesquiterpene Cyclase to Generate an Alcohol Product: Conversion of epi -Isozizaene Synthase into alpha-Bisabolol Synthase.
Authors: Eaton, S.A. / Christianson, D.W.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Database references / Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epi-isozizaene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3159
Polymers43,5961
Non-polymers7198
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.110, 47.098, 75.312
Angle α, β, γ (deg.)90.000, 95.352, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Epi-isozizaene synthase / EIZS / Sesquiterpene cyclase / Sesquiterpene synthase


Mass: 43595.816 Da / Num. of mol.: 1 / Mutation: F95S, F198S
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

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Non-polymers , 6 types, 321 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BisTris (6.4), 0.2 M Ammonium Sulfate, 0.05 M NaF, 31% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.47→29.33 Å / Num. obs: 62835 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.7
Reflection shellResolution: 1.47→1.5 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2934 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→29.33 Å / SU ML: 0.1558 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.6026 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 3851 3.21 %
Rwork0.1706 116033 -
obs0.1714 62835 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.26 Å2
Refinement stepCycle: LAST / Resolution: 1.47→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 43 313 3064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142833
X-RAY DIFFRACTIONf_angle_d1.29833869
X-RAY DIFFRACTIONf_chiral_restr0.0991407
X-RAY DIFFRACTIONf_plane_restr0.0096498
X-RAY DIFFRACTIONf_dihedral_angle_d17.8907996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.490.31151290.29643865X-RAY DIFFRACTION93.19
1.49-1.510.27061420.27464226X-RAY DIFFRACTION97.89
1.51-1.530.34081320.26454059X-RAY DIFFRACTION96.81
1.53-1.550.27451340.25093994X-RAY DIFFRACTION94.81
1.55-1.570.24951330.2374051X-RAY DIFFRACTION95.18
1.57-1.60.21121400.22834134X-RAY DIFFRACTION98.71
1.6-1.620.31411390.22124213X-RAY DIFFRACTION99.09
1.62-1.650.23361400.22164175X-RAY DIFFRACTION98.97
1.65-1.680.28631360.20244237X-RAY DIFFRACTION98.62
1.68-1.710.23131360.20184075X-RAY DIFFRACTION97.3
1.71-1.740.22461330.19834050X-RAY DIFFRACTION95.42
1.74-1.780.23781380.18884189X-RAY DIFFRACTION98.07
1.78-1.820.17651380.17964203X-RAY DIFFRACTION99.13
1.82-1.860.21751340.1794118X-RAY DIFFRACTION99.21
1.86-1.90.20371390.16754204X-RAY DIFFRACTION99.22
1.9-1.960.20651430.17294211X-RAY DIFFRACTION98.69
1.96-2.010.19321370.1664185X-RAY DIFFRACTION99.08
2.01-2.080.17361400.1654201X-RAY DIFFRACTION99.02
2.08-2.150.19241380.16194207X-RAY DIFFRACTION99
2.15-2.240.15271410.14934127X-RAY DIFFRACTION98.96
2.24-2.340.17181370.15654174X-RAY DIFFRACTION98.4
2.34-2.460.17991370.15484173X-RAY DIFFRACTION98.38
2.46-2.620.21351370.16324115X-RAY DIFFRACTION96.94
2.62-2.820.2031350.16814072X-RAY DIFFRACTION96.6
2.82-3.10.19351390.16654220X-RAY DIFFRACTION99.36
3.1-3.550.19221390.16044154X-RAY DIFFRACTION97.81
3.55-4.470.13761400.1394206X-RAY DIFFRACTION99.82
4.47-29.330.17341450.15694195X-RAY DIFFRACTION99.52

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