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- PDB-7kjg: F96M epi-isozizaene synthase: complex with 3 Mg2+ and BTAC -

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Basic information

Entry
Database: PDB / ID: 7kjg
TitleF96M epi-isozizaene synthase: complex with 3 Mg2+ and BTAC
Componentsepi-isozizaene synthase
KeywordsLYASE / terpene cyclase / complex / bisphosphonate inhibitor / risedronate
Function / homology
Function and homology information


epi-isozizaene synthase / epi-isozizaene synthase activity / Lyases; Carbon-oxygen lyases; Acting on phosphates / terpene synthase activity / lyase 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 / PYROPHOSPHATE 2- / Terpene synthase / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRonnebaum, T.A. / Gardner, S.M. / Christianson, D.W.
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: 2020
Title: An Aromatic Cluster in the Active Site of epi -Isozizaene Synthase Is an Electrostatic Toggle for Divergent Terpene Cyclization Pathways.
Authors: Ronnebaum, T.A. / Gardner, S.M. / Christianson, D.W.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: epi-isozizaene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3298
Polymers43,7001
Non-polymers6297
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-41 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.620, 46.950, 75.120
Angle α, β, γ (deg.)90.000, 97.810, 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


Mass: 43700.035 Da / Num. of mol.: 1 / Mutation: F96M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: HCU77_26465 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A6M9XZI2, UniProt: Q9K499*PLUS, epi-isozizaene synthase

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Non-polymers , 6 types, 206 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.08 mM Bis-Tris, pH 5.5, 0.02 mM Bis-Tris, pH 7.5, 0.2 M ammonium sulfate, 30% PEG3350, 0.01 M beta-nicotinamide adenine dinucleotide hydrate

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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: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 4, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→46.95 Å / Num. obs: 84334 / % possible obs: 96.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.3
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 14394 / CC1/2: 0.571

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KB9

3kb9


Resolution: 1.3→45.11 Å / SU ML: 0.1389 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.0942 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1968 2000 2.37 %
Rwork0.1768 82303 -
obs0.1773 84303 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 37 199 2961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462851
X-RAY DIFFRACTIONf_angle_d0.79273895
X-RAY DIFFRACTIONf_chiral_restr0.0694409
X-RAY DIFFRACTIONf_plane_restr0.0047502
X-RAY DIFFRACTIONf_dihedral_angle_d11.37961606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.2671390.24665705X-RAY DIFFRACTION93.68
1.33-1.370.27531400.23715742X-RAY DIFFRACTION94.28
1.37-1.410.26531390.23195745X-RAY DIFFRACTION94.51
1.41-1.450.27911410.21195787X-RAY DIFFRACTION94.83
1.45-1.510.24031400.19265776X-RAY DIFFRACTION94.85
1.51-1.570.23491410.18275817X-RAY DIFFRACTION95.11
1.57-1.640.2191400.17175796X-RAY DIFFRACTION95.9
1.64-1.720.19821440.16035883X-RAY DIFFRACTION96.14
1.72-1.830.18361440.15975922X-RAY DIFFRACTION96.68
1.83-1.970.19951440.16245930X-RAY DIFFRACTION96.92
1.97-2.170.16391440.16315941X-RAY DIFFRACTION97.13
2.17-2.490.17331460.1655986X-RAY DIFFRACTION97.26
2.49-3.130.22911470.1786058X-RAY DIFFRACTION98.1
3.13-45.110.15871510.17266215X-RAY DIFFRACTION98.9

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