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- PDB-5ika: Tobacco 5-epi-aristolochene synthase with PPi -

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Basic information

Entry
Database: PDB / ID: 5ika
TitleTobacco 5-epi-aristolochene synthase with PPi
Components5-epi-aristolochene synthase5-epiaristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / diphosphate
Function / homology
Function and homology information


5-epiaristolochene synthase / 5-epi-aristolochene synthase activity / terpene synthase activity / terpenoid biosynthetic process / magnesium ion binding / cytoplasm
Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Isoprenoid synthase domain superfamily / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpene synthase family, metal binding domain
5-epi-aristolochene synthase
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release

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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)63,4495
Polymers63,2021
Non-polymers2474
Water1,31573
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)126.070, 126.070, 123.390
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-773-

HOH

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Components

#1: Protein/peptide 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 / Magnesium
#3: Chemical ChemComp-DPO / DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPSO, pH 7, 200 mM Mg 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: 2.45→50.73 Å / Num. obs: 37117 / % possible obs: 99.94 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07405 / Net I/σ(I): 14.44
Reflection shellResolution: 2.45→2.537 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5174 / Mean I/σ(I) obs: 2.08 / Num. measured obs: 3618 / % possible all: 99.67

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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: 2.45→50.73 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.27
RfactorNum. reflection% reflection
Rfree0.2161 1844 4.97 %
Rwork0.1744 --
Obs0.1765 37081 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→50.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 12 73 4431
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0084471
f_angle_d1.0536057
f_dihedral_angle_d15.3091647
f_chiral_restr0.035682
f_plane_restr0.005767
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.51630.35581570.2983264299
2.5163-2.59030.29631320.27265799
2.5903-2.67390.24641310.23922678100
2.6739-2.76950.26531250.22342665100
2.7695-2.88030.24921650.21252655100
2.8803-3.01140.21671330.20832691100
3.0114-3.17010.26711370.20642685100
3.1701-3.36870.25341300.20522703100
3.3687-3.62880.23791510.18882702100
3.6288-3.99380.21331350.15752725100
3.9938-4.57140.14991360.13822753100
4.5714-5.75820.21261630.14672759100
5.7582-50.74150.17941490.142922100
Refinement TLS params.

Method: refined / Refinement-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)
12.6733-0.49910.32724.04550.31972.1371-0.0942-0.3106-0.28670.36490.14410.31590.0035-0.1441-0.06220.5089-0.02860.01170.306-0.00680.433532.231155.160123.7678
26.0778-0.5335-4.31555.15283.74277.9242-0.0749-0.4199-0.15920.07140.3908-0.991-0.09311.1792-0.21120.4194-0.0175-0.11550.5177-0.12160.803157.584763.337917.1939
33.6724-1.2981-1.09930.76540.25693.0461-0.11450.23260.0183-0.1680.1986-0.2981-0.06090.2242-0.07570.3618-0.04950.00670.3702-0.10140.449644.384259.45039.4945
43.186-0.8453-0.49026.06181.74371.4970.1096-0.23330.6501-0.1487-0.24971.4276-0.334-0.4430.09630.48910.0090.08530.491-0.14280.993615.682173.420622.7275
52.72760.0934-0.8536.7924-2.69762.32340.0742-0.11570.718-0.07450.0990.8746-0.4284-0.2103-0.28140.59030.0214-0.00170.4118-0.16981.00324.988287.685420.697
63.3169-0.1845-0.6497.1511-2.55814.1861-0.02790.18820.6754-0.7102-0.21890.2951-0.1676-0.13940.03510.51220.03-0.0960.3674-0.12570.822431.435583.629116.0123
71.93551.2369-0.43014.50190.22531.98-0.03170.22270.2312-0.40990.03030.2642-0.06610.00360.00490.41920.04-0.01180.3548-0.07550.588333.508270.984114.4122
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11chain 'A' and (resid 13 through 95 )
22chain 'A' and (resid 96 through 143 )
33chain 'A' and (resid 144 through 222 )
44chain 'A' and (resid 223 through 358 )
55chain 'A' and (resid 359 through 412 )
66chain 'A' and (resid 413 through 472 )
77chain 'A' and (resid 473 through 548 )

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