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- PDB-5ilj: Tobacco 5-epi-aristolochene synthase with BIS-TRIS buffer molecule -

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Basic information

Entry
Database: PDB / ID: 5ilj
TitleTobacco 5-epi-aristolochene synthase with BIS-TRIS buffer molecule
Components5-epi-aristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / BIS-TRIS
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: 2.05 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)63,4112
Polymers63,2021
Non-polymers2091
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.520, 126.520, 122.290
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-986-

HOH

21A-1000-

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-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM BIS-TRIS, pH 6.5, 300 mM Ca Acetate, 16% 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: 2.05→44.73 Å / Num. obs: 54352 / % possible obs: 86.73 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0891 / Net I/σ(I): 11.96
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5194 / Mean I/σ(I) obs: 2.01 / % possible all: 82

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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: 2.05→44.73 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.1883 2690 4.95 %
Rwork0.1596 --
obs0.1611 54338 86.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 14 366 4726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074467
X-RAY DIFFRACTIONf_angle_d0.9766060
X-RAY DIFFRACTIONf_dihedral_angle_d14.5531653
X-RAY DIFFRACTIONf_chiral_restr0.041684
X-RAY DIFFRACTIONf_plane_restr0.004767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.08730.30571340.25792522X-RAY DIFFRACTION82
2.0873-2.12740.2681220.2332550X-RAY DIFFRACTION82
2.1274-2.17080.26921220.21792522X-RAY DIFFRACTION81
2.1708-2.21810.24531210.21122511X-RAY DIFFRACTION81
2.2181-2.26960.23071320.19732524X-RAY DIFFRACTION81
2.2696-2.32640.25041260.18892487X-RAY DIFFRACTION81
2.3264-2.38930.241280.17762521X-RAY DIFFRACTION81
2.3893-2.45960.22051310.17562472X-RAY DIFFRACTION80
2.4596-2.5390.19211480.17472552X-RAY DIFFRACTION83
2.539-2.62970.19051380.17472661X-RAY DIFFRACTION85
2.6297-2.7350.18911320.1722626X-RAY DIFFRACTION85
2.735-2.85940.19841610.16982614X-RAY DIFFRACTION84
2.8594-3.01020.18161330.16672629X-RAY DIFFRACTION84
3.0102-3.19870.19131250.16372617X-RAY DIFFRACTION83
3.1987-3.44560.21191470.16092909X-RAY DIFFRACTION92
3.4456-3.79220.1591760.14433136X-RAY DIFFRACTION100
3.7922-4.34050.14441580.12873204X-RAY DIFFRACTION100
4.3405-5.46710.16711770.13093205X-RAY DIFFRACTION100
5.4671-44.74220.16981790.14163386X-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)
11.74150.3332-0.11793.17790.43421.16940.0099-0.2593-0.15750.3624-0.02260.28470.1247-0.1252-0.00320.3563-0.04330.00610.2298-0.02380.160232.819655.758623.75
25.1968-0.449-2.9944.50863.0033.6689-0.0994-0.2248-0.12790.04240.4341-0.9562-0.04150.6875-0.40920.27460.0045-0.0550.336-0.10430.270357.566864.076316.3025
32.5492-0.3846-0.93851.6890.63452.0001-0.00310.2246-0.0693-0.19370.0497-0.2105-0.01970.0841-0.0260.2085-0.0118-0.00170.2168-0.04610.130344.48659.85959.2447
42.00830.11780.21693.39120.79910.56320.0509-0.0920.25230.0083-0.25641.10990.028-0.27690.10540.2311-0.02660.00930.2923-0.08670.392718.823266.542419.8428
51.52060.43220.21572.54060.50761.23030.0048-0.27190.56330.1247-0.14431.2249-0.1296-0.3440.04490.26280.06170.04580.3178-0.15850.772417.493686.974522.926
62.35490.0891-0.10194.1639-0.10071.7220.02040.05610.3276-0.3081-0.10710.2973-0.2105-0.07520.02960.24340.0176-0.0260.1763-0.06370.215934.972980.920516.5029
73.25321.03810.2027.0279-0.53832.6407-0.10440.27930.1818-0.98270.00730.7509-0.06020.00460.12460.3663-0.0018-0.11140.2889-0.09440.298724.470363.84978.1307
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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