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- PDB-5ikh: Tobacco 5-epi-aristolochene synthase M4 mutant with (-)-premnaspi... -

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Basic information

Entry
Database: PDB / ID: 5ikh
TitleTobacco 5-epi-aristolochene synthase M4 mutant with (-)-premnaspirodiene
Components5-epi-aristolochene synthase5-epiaristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / TEAS-M4 / premnaspirodiene
Function / homology
Function and homology information


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 cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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 cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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-6BW / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoo, H.J. / O'Maille, P.E. / Louie, G.V. / Bowman, M. / Noel, J.P.
CitationJournal: J.Antibiot. / Year: 2016
Title: Biosynthetic potential of sesquiterpene synthases: product profiles of Egyptian Henbane premnaspirodiene synthase and related mutants.
Authors: Koo, H.J. / Vickery, C.R. / Xu, Y. / Louie, G.V. / O'Maille, P.E. / Bowman, M. / Nartey, C.M. / Burkart, M.D. / Noel, J.P.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)63,4634
Polymers63,2101
Non-polymers2533
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.190, 126.190, 122.120
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-880-

HOH

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Components

#1: Protein 5-epi-aristolochene synthase / 5-epiaristolochene synthase / EAS


Mass: 63209.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TEAS (A274T, V372I, Y406L, V516I) / 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-6BW / (2R,5S,10R)-6,10-dimethyl-2-(prop-1-en-2-yl)spiro[4.5]dec-6-ene


Mass: 204.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.85 Å3/Da / Density % sol: 68.09 %
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: Jun 20, 2006 / 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: 2.1→72.05 Å / Num. obs: 57966 / % possible obs: 99.97 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.08277 / Net I/σ(I): 14.47
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 8 % / Rmerge(I) obs: 0.8574 / Mean I/σ(I) obs: 2.22 / Num. measured obs: 5699 / % 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: 2.1→72.047 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.67
RfactorNum. reflection% reflection
Rfree0.2243 1593 2.75 %
Rwork0.1814 --
obs0.1825 57941 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→72.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 17 183 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074756
X-RAY DIFFRACTIONf_angle_d0.9416491
X-RAY DIFFRACTIONf_dihedral_angle_d14.9581814
X-RAY DIFFRACTIONf_chiral_restr0.043719
X-RAY DIFFRACTIONf_plane_restr0.005841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.35791390.31535028X-RAY DIFFRACTION100
2.1678-2.24530.31171440.2595040X-RAY DIFFRACTION100
2.2453-2.33520.26141470.22845056X-RAY DIFFRACTION100
2.3352-2.44150.22681430.20975061X-RAY DIFFRACTION100
2.4415-2.57020.22831430.20095075X-RAY DIFFRACTION100
2.5702-2.73120.22291400.18975065X-RAY DIFFRACTION100
2.7312-2.94210.24471430.18985100X-RAY DIFFRACTION100
2.9421-3.23820.24611470.18295129X-RAY DIFFRACTION100
3.2382-3.70670.22091420.17625158X-RAY DIFFRACTION100
3.7067-4.670.18481460.14855219X-RAY DIFFRACTION100
4.67-72.08910.20571590.15955417X-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)
14.7053-0.5080.6861.7888-0.80821.4621-0.00720.2340.351-0.1452-0.0188-0.0538-0.22230.04960.03040.2664-0.0495-0.02110.4885-0.0760.42898.551934.2668-21.4702
22.72150.04080.86511.7774-0.42811.85360.18690.2522-0.8959-0.0419-0.0183-0.0210.3212-0.0064-0.14570.2778-0.0079-0.1030.3105-0.11690.67142.136313.9541-14.5394
33.26110.32780.12821.3720.1020.6325-0.08860.09410.9613-0.1876-0.01390.4834-0.3001-0.12010.14430.36740.0176-0.16670.3838-0.01590.7315-14.600745.5861-22.0113
45.34521.0253-2.05433.1869-1.52044.43980.0514-0.51490.16320.2463-0.00360.5611-0.3664-0.1861-0.01820.23990.0172-0.09190.4202-0.10380.5625-20.106428.5601-14.1427
57.29842.73722.5955.55571.52684.09480.1121-0.73040.44710.5963-0.30230.3085-0.0278-0.40170.19370.26660.0219-0.0420.3407-0.05260.394-4.336933.1624-14.7293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 412 )
4X-RAY DIFFRACTION4chain 'A' and (resid 413 through 495 )
5X-RAY DIFFRACTION5chain 'A' and (resid 496 through 548 )

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