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- PDB-5il8: Tobacco 5-epi-aristolochene synthase with MOPSO buffer molecule a... -

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Basic information

Entry
Database: PDB / ID: 5il8
TitleTobacco 5-epi-aristolochene synthase with MOPSO buffer molecule and Ca2+ ions
Components5-epi-aristolochene synthase5-epiaristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / MOPSO
Function / homology
Function and homology information


5-epiaristolochene synthase / 5-epi-aristolochene synthase activity / sesquiterpene biosynthetic process / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6BX / Chem-6BY / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKoo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P.
CitationJournal: To Be Published
Title: Small-molecule buffer components can directly affect terpene-synthase activity by interacting with the substrate-binding site of the enzyme
Authors: Koo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: 5-epi-aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7325
Polymers63,2021
Non-polymers5314
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.940, 126.940, 123.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-907-

HOH

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Components

#1: Protein 5-epi-aristolochene synthase / 5-epiaristolochene synthase / EAS


Mass: 63201.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: EAS3, EAS4 / Plasmid: pH9GW / Details (production host): pET28 derived Gateway vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q40577, 5-epiaristolochene synthase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-6BX / (2S)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid


Mass: 225.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO5S
#4: Chemical ChemComp-6BY / (2R)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid


Mass: 225.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 3.96 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPSO, pH 7, 100 mM Ca Acetate, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2013 / Details: mirrors
RadiationMonochromator: double crystal si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.19 Å / Num. obs: 45472 / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.1024 / Net I/σ(I): 8.03
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.6316 / Mean I/σ(I) obs: 1.87 / Num. measured obs: 8429 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IM1
Resolution: 2.3→42.19 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.209 1520 3.38 %
Rwork0.187 --
obs0.187 44993 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 30 211 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074494
X-RAY DIFFRACTIONf_angle_d0.9686093
X-RAY DIFFRACTIONf_dihedral_angle_d16.5521684
X-RAY DIFFRACTIONf_chiral_restr0.036685
X-RAY DIFFRACTIONf_plane_restr0.004769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.25681300.23013835X-RAY DIFFRACTION98
2.3742-2.45910.27311430.21683919X-RAY DIFFRACTION100
2.4591-2.55750.24891300.21363915X-RAY DIFFRACTION100
2.5575-2.67390.28111300.21063926X-RAY DIFFRACTION99
2.6739-2.81490.22971420.20453962X-RAY DIFFRACTION100
2.8149-2.99120.24221340.21033917X-RAY DIFFRACTION99
2.9912-3.2220.24151410.20783952X-RAY DIFFRACTION99
3.222-3.54610.2291400.20143914X-RAY DIFFRACTION98
3.5461-4.05890.22291350.23053832X-RAY DIFFRACTION96
4.0589-5.11240.17921410.14064052X-RAY DIFFRACTION100
5.1124-42.2010.14691540.14214249X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0881-0.46650.10613.66730.17891.2-0.0247-0.0651-0.05050.12330.00771.19170.0736-0.36340.01260.4816-0.09770.05440.39130.0120.817120.769656.831920.3406
22.43111.22990.22634.1670.51021.88970.0807-0.306-0.27580.79640.0961-0.41650.18750.2228-0.16880.52980.0253-0.10430.3089-0.03610.475646.821755.04327.6337
35.9707-0.7571-3.91034.02862.72443.9466-0.0778-0.3818-0.0245-0.0630.3126-0.6668-0.06330.8712-0.26520.3186-0.0024-0.05380.3776-0.09640.508757.735464.060116.3468
41.8217-2.3377-0.98673.83243.29336.24520.07520.07920.1618-0.18270.0449-0.2259-0.28350.1125-0.06060.2229-0.04070.02330.2822-0.04110.35448.840262.96467.0535
51.50230.4029-0.153.04090.30340.8134-0.0143-0.07330.31970.1055-0.01151.0789-0.0974-0.25810.02710.33950.01540.040.3374-0.07410.75520.724975.10820.8356
62.0614-0.1946-0.19175.468-1.6633.93010.0020.13640.3223-0.405-0.01290.329-0.2055-0.1214-0.03380.33450.0097-0.02690.2567-0.06690.500435.304581.110516.6908
75.35762.29950.35062.0648-0.29576.3673-0.29210.57870.495-0.79480.18810.7759-0.49640.10710.05210.4931-0.0421-0.09070.4026-0.09020.657524.641964.05688.3839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 13 THROUGH 57 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 58 THROUGH 97 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 98 THROUGH 143 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 144 THROUGH 195 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 196 THROUGH 412 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 413 THROUGH 519 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 520 THROUGH 548 )

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