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- PDB-7kj8: Wild-type epi-isozizaene synthase: complex with 3 Mg2+ and pamidronate -

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Basic information

Entry
Database: PDB / ID: 7kj8
TitleWild-type epi-isozizaene synthase: complex with 3 Mg2+ and pamidronate
Componentsepi-isozizaene synthase
KeywordsLYASE / terpene cyclase / complex / bisphosphonate inhibitor / pamidronate
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
PAMIDRONATE / Terpene synthase / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)44,1206
Polymers43,7161
Non-polymers4045
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-39 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.540, 46.890, 75.470
Angle α, β, γ (deg.)90.000, 96.690, 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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID


Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H11NO7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
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, 25% 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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→52.18 Å / Num. obs: 88651 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.47 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.3
Reflection shellResolution: 1.9→1.98 Å / Num. unique obs: 1828 / CC1/2: 0.575 / % possible all: 98.3

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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: 1.9→52.18 Å / SU ML: 0.2344 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7128 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2292 3647 7.03 %
Rwork0.185 48238 -
obs0.1881 51885 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→52.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 21 183 2900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582807
X-RAY DIFFRACTIONf_angle_d0.77653846
X-RAY DIFFRACTIONf_chiral_restr0.0449410
X-RAY DIFFRACTIONf_plane_restr0.0057494
X-RAY DIFFRACTIONf_dihedral_angle_d6.22682203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.28841350.24871694X-RAY DIFFRACTION85.87
1.93-1.950.34791360.24911837X-RAY DIFFRACTION89.48
1.95-1.980.31281360.25031779X-RAY DIFFRACTION89.61
1.98-2.010.3471370.25221804X-RAY DIFFRACTION89.65
2.01-2.040.27871410.25651822X-RAY DIFFRACTION89.31
2.04-2.070.25991340.22991803X-RAY DIFFRACTION90.01
2.07-2.110.2781370.23721862X-RAY DIFFRACTION90.82
2.11-2.150.27781410.22591819X-RAY DIFFRACTION90.99
2.15-2.190.27971400.22211831X-RAY DIFFRACTION91.17
2.19-2.230.23481360.20431797X-RAY DIFFRACTION90.2
2.23-2.280.2531380.21191847X-RAY DIFFRACTION90.23
2.28-2.340.27461280.2011793X-RAY DIFFRACTION87.76
2.34-2.390.2391220.19771626X-RAY DIFFRACTION82.1
2.39-2.460.27331370.19571818X-RAY DIFFRACTION89.93
2.46-2.530.25851500.19551907X-RAY DIFFRACTION95.94
2.53-2.610.20191520.18682015X-RAY DIFFRACTION96.18
2.61-2.710.26781440.19461893X-RAY DIFFRACTION97.14
2.71-2.810.23551480.17891952X-RAY DIFFRACTION96.55
2.81-2.940.21641550.18431987X-RAY DIFFRACTION96.84
2.94-3.10.2141400.18471915X-RAY DIFFRACTION96.48
3.1-3.290.26791440.16841953X-RAY DIFFRACTION96.37
3.29-3.550.19191470.16521925X-RAY DIFFRACTION96.06
3.55-3.90.19441450.14691910X-RAY DIFFRACTION94.35
3.9-4.470.1751340.13891766X-RAY DIFFRACTION88.29
4.47-5.630.16191430.16091880X-RAY DIFFRACTION93.66
5.63-52.180.20551470.16612003X-RAY DIFFRACTION98.26

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