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- PDB-5ilk: Tobacco 5-epi-aristolochene synthase with partial density from MO... -

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Basic information

Entry
Database: PDB / ID: 5ilk
TitleTobacco 5-epi-aristolochene synthase with partial density from MOPSO or BIS-TRIS buffer molecule in the active site
Components5-epi-aristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / MOPSO / 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 / 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: 2.35 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


Theoretical massNumber of molelcules
Total (without water)63,2021
Polymers63,2021
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.960, 126.960, 123.110
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-744-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: Reservoir: 100 mM MOPSO, pH 7, 300 mM Mg Acetate, 13% PEG 8000 Soaked in 50 mM MOPSO (pH 7), 10 mM BIS-TRIS (pH 6.5) 110 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: 2.35→50.77 Å / Num. obs: 35665 / % possible obs: 83.97 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09516 / Net I/σ(I): 10.1
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.52 / % possible all: 64.51

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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: 2.35→50.767 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.31
RfactorNum. reflection% reflection
Rfree0.24 1789 5.05 %
Rwork0.2011 --
obs0.2031 35423 83.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→50.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 0 144 4490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084454
X-RAY DIFFRACTIONf_angle_d0.9816044
X-RAY DIFFRACTIONf_dihedral_angle_d15.1441645
X-RAY DIFFRACTIONf_chiral_restr0.035682
X-RAY DIFFRACTIONf_plane_restr0.004767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.41350.2892890.24181987X-RAY DIFFRACTION65
2.4135-2.48460.28531260.21611931X-RAY DIFFRACTION64
2.4846-2.56480.253990.21911954X-RAY DIFFRACTION64
2.5648-2.65640.2521130.21151928X-RAY DIFFRACTION64
2.6564-2.76280.23471050.21432067X-RAY DIFFRACTION67
2.7628-2.88850.29421740.2292796X-RAY DIFFRACTION92
2.8885-3.04080.2641430.23492839X-RAY DIFFRACTION92
3.0408-3.23120.27141390.23072825X-RAY DIFFRACTION91
3.2312-3.48070.2931420.22772819X-RAY DIFFRACTION91
3.4807-3.83080.31881590.29242895X-RAY DIFFRACTION93
3.8308-4.38490.19451490.17563101X-RAY DIFFRACTION99
4.3849-5.52350.17771770.14583175X-RAY DIFFRACTION100
5.5235-50.77920.19211740.14313317X-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)
10.46490.3228-0.49393.14430.45630.92540.1044-0.1912-0.07530.3907-0.01890.5610.1346-0.173-0.0350.3688-0.06650.02380.2646-0.01880.492228.75255.323321.4197
20.31410.70140.74053.66180.43.27250.2228-0.2569-0.32920.62950.0372-0.63210.2450.5237-0.24410.40880.0461-0.17650.2696-0.07540.372849.880859.621326.0585
31.2017-0.5695-0.34863.22562.13773.9-0.03530.06380.0824-0.28390.1447-0.5505-0.3490.4467-0.11420.2862-0.04370.05030.2958-0.09590.348452.67464.13399.3451
42.13130.48620.14024.8111-0.17811.99990.06920.1166-0.3869-0.2443-0.0762-0.15140.21750.15710.05430.2648-0.01330.0320.1977-0.09650.354137.071554.702513.4841
51.99490.5473-0.07144.30650.13890.97910.0402-0.07660.4653-0.071-0.13941.0958-0.1351-0.22040.05190.27070.04540.00510.2648-0.11340.557424.115879.194819.8694
63.54281.20960.26468.3155-1.21214.2044-0.07750.3870.0966-0.9602-0.23440.6615-0.28210.19260.25190.4295-0.0255-0.12040.3403-0.09080.372424.623464.07128.2146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 519 )
6X-RAY DIFFRACTION6chain 'A' and (resid 520 through 548 )

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