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- PDB-7kje: F96S epi-isozizaene synthase: complex with 3 Mg2+ and neridronate -

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Basic information

Entry
Database: PDB / ID: 7kje
TitleF96S epi-isozizaene synthase: complex with 3 Mg2+ and neridronate
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 / 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
Chem-NRD / Terpene synthase / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRonnebaum, T.A. / Gardner, S. / 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)44,1026
Polymers43,6561
Non-polymers4465
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-45 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.680, 76.230, 108.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein epi-isozizaene synthase /


Mass: 43655.914 Da / Num. of mol.: 1 / Mutation: F96S
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NRD / (6-azanyl-1-oxidanyl-1-phosphono-hexyl)phosphonic acid / Neridronic acid


Mass: 277.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H17NO7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.05 mM Bis-Tris, pH 5.5, 0.05 mM Bis-Tris, pH 7.5, 0.2 M ammonium sulfate, 26% PEG3350, 4% v/v 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→62.34 Å / Num. obs: 51746 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.66 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.9
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 2540 / CC1/2: 0.692

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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 6AXO

6axo


Resolution: 1.6→62.34 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.6832 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2099 5110 3.87 %
Rwork0.1889 94030 -
obs0.1898 51644 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→62.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 24 249 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582657
X-RAY DIFFRACTIONf_angle_d0.8213638
X-RAY DIFFRACTIONf_chiral_restr0.0464388
X-RAY DIFFRACTIONf_plane_restr0.0053472
X-RAY DIFFRACTIONf_dihedral_angle_d6.63152043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.27931360.29463522X-RAY DIFFRACTION99.38
1.62-1.640.32121380.27543428X-RAY DIFFRACTION99.22
1.64-1.660.29431430.27213526X-RAY DIFFRACTION99.19
1.66-1.690.28421380.26013463X-RAY DIFFRACTION99.12
1.69-1.710.32881410.25633437X-RAY DIFFRACTION98.4
1.71-1.740.26071420.25483525X-RAY DIFFRACTION99.62
1.74-1.770.25711400.23793487X-RAY DIFFRACTION99.59
1.77-1.80.23551430.22573515X-RAY DIFFRACTION99.27
1.8-1.830.22021320.21773412X-RAY DIFFRACTION98.72
1.83-1.870.22631400.21163501X-RAY DIFFRACTION98.91
1.87-1.90.25461330.21713491X-RAY DIFFRACTION99.23
1.9-1.950.22871420.21783496X-RAY DIFFRACTION98.46
1.95-1.990.2351390.19943383X-RAY DIFFRACTION98.6
1.99-2.040.20391400.19293528X-RAY DIFFRACTION99.7
2.04-2.10.22471420.17663493X-RAY DIFFRACTION99.48
2.1-2.160.22271380.16993469X-RAY DIFFRACTION99.61
2.16-2.230.23251440.17613518X-RAY DIFFRACTION99.78
2.23-2.310.19981400.17113484X-RAY DIFFRACTION99.62
2.31-2.40.18481430.17023450X-RAY DIFFRACTION99.5
2.4-2.510.22121430.17593523X-RAY DIFFRACTION99.59
2.51-2.640.24761410.18033496X-RAY DIFFRACTION99.53
2.64-2.810.17531410.18313500X-RAY DIFFRACTION99.48
2.81-3.020.20881430.17443479X-RAY DIFFRACTION99.72
3.02-3.330.17951390.17553537X-RAY DIFFRACTION99.86
3.33-3.810.16821410.15643351X-RAY DIFFRACTION96.68
3.81-4.80.17411420.16113503X-RAY DIFFRACTION100
4.8-62.340.19531440.19983513X-RAY DIFFRACTION99.84

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