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- PDB-5uv0: Crystal Structure of (+)-Limonene Synthase from Citrus sinensis -

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Basic information

Entry
Database: PDB / ID: 5uv0
TitleCrystal Structure of (+)-Limonene Synthase from Citrus sinensis
Components(+)-limonene synthase
KeywordsLYASE / Terpene synthase / enantiomer / terpene synthase fold / monoterpene
Function / homology
Function and homology information


(R)-limonene synthase / (R)-limonene synthase activity / diterpenoid biosynthetic process / chloroplast / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / 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 ...Terpene cyclase-like 1, C-terminal domain / 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
(R)-limonene synthase 1, chloroplastic
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsPrem Kumar, R. / Oprian, D.D.
CitationJournal: Biochemistry / Year: 2017
Title: Functional and Structural Characterization of a (+)-Limonene Synthase from Citrus sinensis.
Authors: Morehouse, B.R. / Kumar, R.P. / Matos, J.O. / Olsen, S.N. / Entova, S. / Oprian, D.D.
History
DepositionFeb 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Oct 4, 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: (+)-limonene synthase


Theoretical massNumber of molelcules
Total (without water)70,4411
Polymers70,4411
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.790, 85.790, 216.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-755-

HOH

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Components

#1: Protein (+)-limonene synthase


Mass: 70441.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: A0A1C9J6A7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.83 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG8000, 100 mM Tris pH 7.5, 350 mM sodium tartrate
PH range: 7.5-9.0 / Temp details: 20

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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 315 / Detector: CCD / Date: Oct 30, 2014 / 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→20 Å / Num. obs: 36820 / % possible obs: 99.8 % / Redundancy: 20.7 % / Biso Wilson estimate: 49.92 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXdev_2294refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ONG

2ong


Resolution: 2.3→19.992 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2287 1775 4.84 %
Rwork0.1902 --
obs0.192 36688 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.79 Å2 / Biso mean: 56.8622 Å2 / Biso min: 31.21 Å2
Refinement stepCycle: final / Resolution: 2.3→19.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 0 174 4490
Biso mean---55.85 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074426
X-RAY DIFFRACTIONf_angle_d0.8195989
X-RAY DIFFRACTIONf_chiral_restr0.044646
X-RAY DIFFRACTIONf_plane_restr0.005755
X-RAY DIFFRACTIONf_dihedral_angle_d15.1582621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.36210.29821290.26052598272799
2.3621-2.43150.27561400.252226482788100
2.4315-2.50980.31431360.236426242760100
2.5098-2.59930.27991430.226926432786100
2.5993-2.70320.26831260.233426632789100
2.7032-2.82590.23621370.22526502787100
2.8259-2.97440.29261270.226426642791100
2.9744-3.16010.26631500.238526492799100
3.1601-3.4030.28421310.217226972828100
3.403-3.74340.20081170.192927002817100
3.7434-4.28050.21091510.170527012852100
4.2805-5.37550.19041300.150727722902100
5.3755-19.99240.1981580.159429043062100

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