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- PDB-7kj9: Wild-type epi-isozizaene synthase: complex with 3 Mg2+ and risedronate -

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Basic information

Entry
Database: PDB / ID: 7kj9
TitleWild-type epi-isozizaene synthase: complex with 3 Mg2+ and risedronate
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-RIS / Terpene synthase / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)44,1686
Polymers43,7161
Non-polymers4525
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-40 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.980, 47.030, 75.470
Angle α, β, γ (deg.)90.000, 96.060, 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

#1: Protein epi-isozizaene synthase /


Mass: 43716.012 Da / Num. of mol.: 1
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-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate / Risedronic acid


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.06 mM Bis-Tris, pH 5.5, 0.04 mM Bis-Tris, pH 7.5, 0.2 M ammonium sulfate, 27% PEG3350

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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: 2.2→75.05 Å / Num. obs: 18422 / % possible obs: 97 % / Redundancy: 2.8 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 0.919 / Net I/σ(I): 4.3
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 1545 / CC1/2: 0.606

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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: 2.2→75.05 Å / SU ML: 0.3017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7345 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2806 1840 9.96 %
Rwork0.2176 29117 -
obs0.2239 18373 87.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→75.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 25 90 2790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072793
X-RAY DIFFRACTIONf_angle_d0.85793824
X-RAY DIFFRACTIONf_chiral_restr0.0495403
X-RAY DIFFRACTIONf_plane_restr0.0064493
X-RAY DIFFRACTIONf_dihedral_angle_d7.16892167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.36281330.2631215X-RAY DIFFRACTION84.14
2.23-2.270.31241300.25591151X-RAY DIFFRACTION83.13
2.27-2.310.32321330.2571200X-RAY DIFFRACTION80.69
2.31-2.340.29731210.23151148X-RAY DIFFRACTION78.19
2.34-2.390.31651090.2486992X-RAY DIFFRACTION71.03
2.39-2.430.29961200.2421109X-RAY DIFFRACTION75.68
2.43-2.480.31941410.23291238X-RAY DIFFRACTION87
2.48-2.540.29831540.22921359X-RAY DIFFRACTION93.57
2.54-2.60.32691510.23921321X-RAY DIFFRACTION94.12
2.6-2.660.36961510.25491346X-RAY DIFFRACTION93.62
2.66-2.730.33551550.25021380X-RAY DIFFRACTION95.05
2.73-2.810.36591540.23911368X-RAY DIFFRACTION93.78
2.81-2.90.32581490.23121323X-RAY DIFFRACTION93.11
2.9-3.010.26731490.21181378X-RAY DIFFRACTION94.73
3.01-3.130.25641440.20051380X-RAY DIFFRACTION94.37
3.13-3.270.26591440.21361336X-RAY DIFFRACTION93.73
3.27-3.440.29011470.22671315X-RAY DIFFRACTION91.95
3.44-3.660.24461420.20411317X-RAY DIFFRACTION91.99
3.66-3.940.23641350.19571274X-RAY DIFFRACTION87.14
3.94-4.340.22471290.18381146X-RAY DIFFRACTION80.44
4.34-4.970.21211220.19481126X-RAY DIFFRACTION78.2
4.97-6.260.28061560.19651346X-RAY DIFFRACTION93.35
6.26-75.050.20881510.18921349X-RAY DIFFRACTION93.52

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