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- PDB-7kjf: Wild-type epi-isozizaene synthase: complex with 3 Mg2+ and neridronate -

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Basic information

Entry
Database: PDB / ID: 7kjf
TitleWild-type 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 / 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
Chem-NRD / Terpene synthase / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)44,53110
Polymers43,7161
Non-polymers8159
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-34 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.530, 46.760, 74.820
Angle α, β, γ (deg.)90.000, 98.340, 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: 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

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Non-polymers , 5 types, 237 molecules

#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


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


Mass: 277.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H17NO7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.04 Å3/Da / Density % sol: 39.71 %
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, 27% PEG3350, 0.01 M L-Proline

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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 EIGER2 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: 1.4→46.76 Å / Num. obs: 69464 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 11.37 Å2 / CC1/2: 0.994 / Net I/σ(I): 6.3
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 3544 / CC1/2: 0.559

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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: 1.4→45.16 Å / SU ML: 0.1839 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8854 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2391 1999 2.88 %
Rwork0.1941 67431 -
obs0.1954 69430 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.09 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 48 228 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542916
X-RAY DIFFRACTIONf_angle_d0.80293985
X-RAY DIFFRACTIONf_chiral_restr0.069414
X-RAY DIFFRACTIONf_plane_restr0.0056509
X-RAY DIFFRACTIONf_dihedral_angle_d9.92981641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.33511410.27894772X-RAY DIFFRACTION99.98
1.44-1.470.29851420.25964795X-RAY DIFFRACTION99.8
1.47-1.520.28521440.23794803X-RAY DIFFRACTION99.86
1.52-1.570.27941410.22384767X-RAY DIFFRACTION99.51
1.57-1.620.27351420.2114792X-RAY DIFFRACTION99.76
1.62-1.690.28471420.2084785X-RAY DIFFRACTION99.84
1.69-1.760.25461420.19964803X-RAY DIFFRACTION99.86
1.76-1.860.22891420.19154804X-RAY DIFFRACTION99.82
1.86-1.970.22831430.18624837X-RAY DIFFRACTION99.76
1.97-2.130.23521420.17564804X-RAY DIFFRACTION99.8
2.13-2.340.22771430.17434813X-RAY DIFFRACTION99.16
2.34-2.680.21161430.18124813X-RAY DIFFRACTION99.74
2.68-3.370.22061440.18534864X-RAY DIFFRACTION99.94
3.37-45.160.22611480.18784979X-RAY DIFFRACTION99.96

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