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- PDB-5ik6: Tobacco 5-epi-aristolochene synthase with germacrene A and PPi -

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Basic information

Entry
Database: PDB / ID: 5ik6
TitleTobacco 5-epi-aristolochene synthase with germacrene A and PPi
Components5-epi-aristolochene synthase5-epiaristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / germacrene A / diphosphate
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
GERMACRENE A / DIPHOSPHATE / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKoo, H.J. / Xu, Y. / 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)63,6536
Polymers63,2021
Non-polymers4515
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.510, 126.510, 123.210
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-925-

HOH

31A-930-

HOH

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Components

#1: Protein 5-epi-aristolochene synthase / 5-epiaristolochene 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.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CRE / GERMACRENE A / 8-ISOPROPENYL-1,5-DIMETHYL-CYCLODECA-1,5-DIENE / Germacrene


Mass: 204.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24 / Comment: Antimicrobial*YM
#4: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 3.91 Å3/Da / Density % sol: 68.53 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPSO, pH 7, 300 mM Mg Acetate, 13% 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: 2.3→44.13 Å / Num. obs: 42184 / % possible obs: 93.82 % / Redundancy: 6 % / Rmerge(I) obs: 0.08375 / Net I/σ(I): 12.24
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5803 / Mean I/σ(I) obs: 3.09 / Num. measured obs: 3738

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata scaling
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IM1
Resolution: 2.3→44.13 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.1999 2099 4.98 %
Rwork0.1626 --
obs0.1645 42147 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 27 235 4608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084488
X-RAY DIFFRACTIONf_angle_d1.0096076
X-RAY DIFFRACTIONf_dihedral_angle_d14.6461647
X-RAY DIFFRACTIONf_chiral_restr0.036683
X-RAY DIFFRACTIONf_plane_restr0.005770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35350.30941240.24682373X-RAY DIFFRACTION85
2.3535-2.41240.29171090.22522368X-RAY DIFFRACTION84
2.4124-2.47760.23471420.2052342X-RAY DIFFRACTION84
2.4776-2.55050.2571210.2022342X-RAY DIFFRACTION84
2.5505-2.63280.22391260.18992348X-RAY DIFFRACTION83
2.6328-2.72690.19861190.19772428X-RAY DIFFRACTION87
2.7269-2.8360.23251530.18372818X-RAY DIFFRACTION100
2.836-2.96510.22351530.19192807X-RAY DIFFRACTION100
2.9651-3.12140.22531380.18232826X-RAY DIFFRACTION100
3.1214-3.31690.24661450.18072847X-RAY DIFFRACTION100
3.3169-3.57290.21511560.16952824X-RAY DIFFRACTION100
3.5729-3.93220.18831400.15712855X-RAY DIFFRACTION100
3.9322-4.50080.15011450.12862898X-RAY DIFFRACTION100
4.5008-5.66860.17191710.1332899X-RAY DIFFRACTION100
5.6686-44.14120.16331570.13093073X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3846-0.0147-0.15853.85550.41391.26650.0129-0.2701-0.2770.43320.02330.39480.1146-0.1237-0.05230.4084-0.04790.00970.2787-0.01060.220932.902355.648923.8741
26.98940.1141-3.70864.90793.01665.6152-0.0707-0.428-0.1310.05240.409-0.9264-0.05580.9447-0.22510.26990.0107-0.09050.3514-0.08690.353657.645463.953616.3995
33.6164-1.2145-0.73726.51893.50925.4696-0.02120.29390.1343-0.21110.0524-0.3108-0.1690.1661-0.01120.2401-0.04510.01810.272-0.02950.16648.725962.72437.0721
44.2780.01480.58677.2374-2.58823.9711-0.04060.1043-0.4414-0.46870.1018-0.26910.26570.0482-0.07290.2132-0.03820.02130.2402-0.07050.165337.057354.393113.5239
51.83980.44060.01783.53770.45870.83930.0046-0.20790.58030.0293-0.15521.4136-0.1842-0.34980.07870.34690.03990.02310.36-0.14810.731718.19777.743821.8685
63.0812-0.1204-0.32115.0968-0.6923.31580.05320.2010.3569-0.4288-0.11490.3443-0.2459-0.13140.03060.30380.0272-0.03470.2072-0.07090.303735.102280.748316.6721
77.98772.2212-0.19243.3-4.79938.9017-0.28870.50050.5672-0.7737-0.02240.5216-0.3754-0.13960.28070.48010.0078-0.1070.379-0.13280.362124.561563.82828.2854
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 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 412 )
6X-RAY DIFFRACTION6chain 'A' and (resid 413 through 519 )
7X-RAY DIFFRACTION7chain 'A' and (resid 520 through 548 )

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