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- PDB-5il3: Tobacco 5-epi-aristolochene synthase with MOPSO buffer molecule a... -

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Basic information

Entry
Database: PDB / ID: 5il3
TitleTobacco 5-epi-aristolochene synthase with MOPSO buffer molecule and Mg2+ ions
Components5-epi-aristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / MOPSO
Function / homology
Function and homology information


(+)-2-epi-prezizaene synthase / (-)-alpha-cedrene synthase / 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 synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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 ...Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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: 1.85 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,7015
Polymers63,2021
Non-polymers4994
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.730, 126.730, 123.050
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-1131-

HOH

21A-1146-

HOH

31A-1154-

HOH

41A-1158-

HOH

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Components

#1: Protein 5-epi-aristolochene 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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


Mass: 18.015 Da / Num. of mol.: 471 / 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: 3.92 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPSO, pH 7, 100 mM Mg 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: 1.85→42.1 Å / Num. obs: 85647 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.76
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 11 % / Rmerge(I) obs: 1.66 / Mean I/σ(I) obs: 1.59 / Num. measured obs: 8429 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IM1

5im1


Resolution: 1.85→42.1 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.187 1732 2.02 %
Rwork0.167 --
obs0.167 85621 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 30 471 4850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064490
X-RAY DIFFRACTIONf_angle_d0.9016093
X-RAY DIFFRACTIONf_dihedral_angle_d13.7361684
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 (%)
1.85-1.90450.34071480.336893X-RAY DIFFRACTION100
1.9045-1.96590.34231400.2846883X-RAY DIFFRACTION100
1.9659-2.03620.27511450.2246894X-RAY DIFFRACTION100
2.0362-2.11770.22081490.19916913X-RAY DIFFRACTION100
2.1177-2.21410.22731440.18416916X-RAY DIFFRACTION100
2.2141-2.33080.21611410.17876939X-RAY DIFFRACTION100
2.3308-2.47680.18171370.17236955X-RAY DIFFRACTION100
2.4768-2.6680.20631420.17246972X-RAY DIFFRACTION100
2.668-2.93650.1631460.17027003X-RAY DIFFRACTION100
2.9365-3.36120.20831420.16697024X-RAY DIFFRACTION100
3.3612-4.23420.14991440.14187121X-RAY DIFFRACTION100
4.2342-42.11250.1541540.13827376X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.42890.6088-0.08693.56250.44491.26320.0335-0.2119-0.04340.3578-0.02940.42850.1018-0.1349-0.05610.3432-0.03530.02580.2131-0.01310.233632.860355.878923.7131
25.0713-0.3965-3.27363.84133.59417.39170.021-0.23730.0071-0.03440.427-0.6579-0.14170.8804-0.31290.2337-0.0035-0.05410.299-0.07560.29157.604463.955816.3262
31.936-0.681-0.45765.2373.54184.1802-0.02250.22870.0268-0.25570.086-0.1839-0.17230.1286-0.07970.2335-0.04310.01440.2732-0.01730.175348.749162.84167.0237
43.26850.12450.22996.8098-1.56483.1273-0.03460.1444-0.3598-0.27590.1025-0.02180.2484-0.0051-0.04810.2049-0.0233-0.00760.2164-0.04720.198537.08754.513213.4924
52.00050.06110.00663.3660.97130.8068-0.0093-0.060.1667-0.0237-0.15521.206-0.0441-0.28880.12240.2616-0.02570.02260.2829-0.06190.556718.970466.599619.9839
61.68220.5655-0.19053.7191-0.0161.0864-0.0104-0.18150.47890.1731-0.0821.2265-0.1973-0.25290.01370.27440.05670.03470.2654-0.11570.70721.483885.386522.4104
71.66460.6763-0.15323.83630.36011.0475-0.05840.22160.2566-0.58770.03030.5108-0.197-0.10920.00540.32540.026-0.05960.2436-0.01790.271333.436675.514812.0433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 13 THROUGH 97 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 98 THROUGH 143 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 144 THROUGH 195 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 196 THROUGH 222 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 223 THROUGH 306 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 307 THROUGH 454 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 455 THROUGH 548 )

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