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- PDB-5ilz: Tobacco 5-epi-aristolochene synthase with BIS-TRIS propane (BTP) ... -

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Basic information

Entry
Database: PDB / ID: 5ilz
TitleTobacco 5-epi-aristolochene synthase with BIS-TRIS propane (BTP) buffer molecule
Components5-epi-aristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / BIS-TRIS propane / BTP
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 / 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: 1.92 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 5, 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)63,4842
Polymers63,2021
Non-polymers2821
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.030, 125.030, 117.540
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-735-

HOH

21A-889-

HOH

31A-1198-

HOH

41A-1225-

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-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM BTP, pH 7, 75 mM Li Citrate, 12% 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: 1.92→41.38 Å / Num. obs: 71347 / % possible obs: 99.89 % / Redundancy: 11.4 % / CC1/2: 0.949 / Rmerge(I) obs: 0.4594 / Net I/σ(I): 4.62
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.406 / Mean I/σ(I) obs: 0.69 / % possible all: 99.6

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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: 1.92→41.375 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.2159 1934 2.79 %
Rwork0.1829 --
obs0.1838 69385 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→41.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 19 564 4932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074475
X-RAY DIFFRACTIONf_angle_d1.0936071
X-RAY DIFFRACTIONf_dihedral_angle_d14.8311659
X-RAY DIFFRACTIONf_chiral_restr0.09684
X-RAY DIFFRACTIONf_plane_restr0.004768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.9680.33671080.29984096X-RAY DIFFRACTION84
1.968-2.02120.30611160.28094312X-RAY DIFFRACTION88
2.0212-2.08070.32741290.24854551X-RAY DIFFRACTION93
2.0807-2.14790.23081420.22454738X-RAY DIFFRACTION97
2.1479-2.22460.26811430.21564816X-RAY DIFFRACTION99
2.2246-2.31370.24451430.21044905X-RAY DIFFRACTION100
2.3137-2.4190.23881370.19744919X-RAY DIFFRACTION100
2.419-2.54650.24631410.19614914X-RAY DIFFRACTION100
2.5465-2.7060.24841500.18824922X-RAY DIFFRACTION100
2.706-2.91490.21291360.18114964X-RAY DIFFRACTION100
2.9149-3.20820.20991460.17894960X-RAY DIFFRACTION100
3.2082-3.67210.18261390.16365021X-RAY DIFFRACTION100
3.6721-4.62550.17691490.14195051X-RAY DIFFRACTION100
4.6255-41.38510.1771550.15865282X-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)
12.1549-0.39220.07832.08090.20461.3514-0.0957-0.1382-0.13690.24830.03990.11480.1392-0.10520.03820.2817-0.02260.01260.1413-0.05070.149931.650655.533423.2957
24.9811-0.1943-2.12872.75872.92433.8446-0.0761-0.06850.14740.05650.5401-0.54020.05030.8459-0.29460.17140.0064-0.05030.3123-0.12530.283556.571563.290216.2839
31.72030.0628-0.88051.55830.52392.0251-0.04110.1224-0.1152-0.06130.0861-0.15450.04120.1557-0.0450.1120.00420.00440.1427-0.05020.169743.715859.05139.0771
41.2868-1.2416-0.0364.14430.07060.6940.1030.0629-0.0976-0.2239-0.12640.57440.0599-0.22240.01120.1805-0.02830.02420.1824-0.0680.258917.937366.138618.8022
51.30910.475-0.43821.9621-0.68341.56660.0017-0.02660.30390.1110.11950.4676-0.2085-0.3078-0.10690.25620.05750.07660.1754-0.04270.375315.933387.626120.6604
63.19570.7486-2.01113.2735-0.19526.1495-0.03280.00020.2582-0.13-0.05440.2157-0.2382-0.15180.07040.15770.01440.01840.0567-0.08150.265229.679380.109519.9631
72.4556-0.72460.015.7292-2.45676.08270.34580.62110.3417-0.9773-0.18510.0891-0.17890.0206-0.050.38880.02170.03650.23280.01220.258137.799285.27796.364
83.23462.07351.23923.64321.82442.399-0.15550.33080.0594-0.44610.08370.2239-0.25370.0140.09770.20390.0175-0.00450.1514-0.05090.178628.910366.762214.4069
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 402 )
6X-RAY DIFFRACTION6chain 'A' and (resid 403 through 454 )
7X-RAY DIFFRACTION7chain 'A' and (resid 455 through 495 )
8X-RAY DIFFRACTION8chain 'A' and (resid 496 through 548 )

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