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- PDB-5ild: Tobacco 5-epi-aristolochene synthase with MES buffer molecule and... -

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Basic information

Entry
Database: PDB / ID: 5ild
TitleTobacco 5-epi-aristolochene synthase with MES buffer molecule and Mg2+ ions
Components5-epi-aristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / MES
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
5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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)63,4464
Polymers63,2021
Non-polymers2443
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.910, 126.910, 123.190
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-883-

HOH

21A-889-

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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 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: 2.12→42.16 Å / Num. obs: 57249 / % possible obs: 99.55 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08166 / Net I/σ(I): 13.17
Reflection shellResolution: 2.12→2.196 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.5387 / Mean I/σ(I) obs: 2.36 / % possible all: 100

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Processing

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

5im1


Resolution: 2.12→42.16 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3
RfactorNum. reflection% reflection
Rfree0.2009 1997 3.49 %
Rwork0.1731 --
obs0.1741 57165 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 14 196 4556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084483
X-RAY DIFFRACTIONf_angle_d0.9346079
X-RAY DIFFRACTIONf_dihedral_angle_d15.2281664
X-RAY DIFFRACTIONf_chiral_restr0.036683
X-RAY DIFFRACTIONf_plane_restr0.004767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.1730.28091370.27033869X-RAY DIFFRACTION100
2.173-2.23180.32191470.25133908X-RAY DIFFRACTION100
2.2318-2.29750.26761410.24533909X-RAY DIFFRACTION100
2.2975-2.37160.25581450.21363902X-RAY DIFFRACTION100
2.3716-2.45640.26581400.20223920X-RAY DIFFRACTION100
2.4564-2.55470.19261400.18983897X-RAY DIFFRACTION100
2.5547-2.67090.22831390.19463927X-RAY DIFFRACTION100
2.6709-2.81170.20631470.19423926X-RAY DIFFRACTION100
2.8117-2.98790.25931370.20093933X-RAY DIFFRACTION100
2.9879-3.21850.23171440.19323941X-RAY DIFFRACTION100
3.2185-3.54220.20691430.17963955X-RAY DIFFRACTION99
3.5422-4.05440.1881440.15273946X-RAY DIFFRACTION99
4.0544-5.10670.16161430.13584001X-RAY DIFFRACTION99
5.1067-42.16830.15231500.14344134X-RAY DIFFRACTION97
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)
11.35210.1191-0.25574.25070.34031.5857-0.0055-0.2788-0.14020.50040.0080.38890.1019-0.1631-0.0340.4765-0.0621-0.02460.2795-0.01770.448733.007355.836723.8989
26.2099-0.6791-4.00383.8072.94964.6662-0.0298-0.4821-0.1142-0.02090.3358-1.124-0.17121.076-0.36210.3871-0.0228-0.1010.4222-0.09610.712257.716664.046716.4144
33.1305-0.5634-0.8821.47120.23942.5529-0.04870.2244-0.1042-0.05860.0914-0.3581-0.02290.1258-0.03260.2751-0.0306-0.02260.2633-0.07150.383244.648359.97079.3508
42.85080.21530.04544.20070.90141.12840.006-0.02240.3269-0.0386-0.21561.1968-0.0457-0.35820.15380.3707-0.04130.00310.3451-0.10390.672618.948966.691220.1205
51.76560.5403-0.08563.0608-0.21671.37930.0458-0.2260.70840.1903-0.02521.3045-0.143-0.3612-0.02350.46490.05250.04520.4157-0.15941.162817.628587.135623.3288
62.69910.2281-0.4575.7374-1.31883.50230.06570.12360.4462-0.3323-0.06810.2366-0.2648-0.0983-0.03590.36030.0091-0.04990.2397-0.08380.515635.182281.080116.7439
79.13393.1033-1.06256.9695-6.66318.4321-0.19590.69850.5285-0.59240.1590.7839-0.2446-0.0791-0.03070.477-0.0278-0.09540.4087-0.12770.522924.630564.0938.293
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 222 )
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 306 )
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 412 )
6X-RAY DIFFRACTION6chain 'A' and (resid 413 through 519 )
7X-RAY DIFFRACTION7chain 'A' and (resid 520 through 548 )

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