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- PDB-5uv1: Crystal Structure of (+)-Limonene Synthase Complexed with 2-Fluor... -

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Basic information

Entry
Database: PDB / ID: 5uv1
TitleCrystal Structure of (+)-Limonene Synthase Complexed with 2-Fluorogeranyl Diphosphate
Components(+)-limonene synthase
KeywordsLYASE / Terpene synthase / enantiomer / terpene synthase fold / monoterpene / fluorinated analog
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 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 ...Terpene cyclase-like 1, C-terminal domain / 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
Chem-0FV / : / (R)-limonene synthase 1, chloroplastic
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPrem Kumar, R. / Malik, K. / Oprian, D.D.
CitationJournal: Biochemistry / Year: 2017
Title: Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed by (+)-Limonene Synthase from Citrus sinensis Using Fluorinated Substrate Analogues.
Authors: Kumar, R.P. / Morehouse, B.R. / Matos, J.O. / Malik, K. / Lin, H. / Krauss, I.J. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (+)-limonene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9385
Polymers70,4411
Non-polymers4974
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)85.510, 85.510, 215.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-0FV / (2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate / 2-fluorogeranyl diphosphate


Mass: 332.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H19FO7P2
#4: 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: 2.8 Å3/Da / Density % sol: 55.99 %
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

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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: Apr 28, 2016 / 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: 2.2→20 Å / Num. obs: 31630 / % possible obs: 98.7 % / Redundancy: 26.9 % / Biso Wilson estimate: 55.93 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_2650refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UV0

5uv0


Resolution: 2.4→19.925 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.23
RfactorNum. reflection% reflection
Rfree0.2355 1549 4.95 %
Rwork0.2027 --
obs0.2043 31273 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.06 Å2 / Biso mean: 66.912 Å2 / Biso min: 34.62 Å2
Refinement stepCycle: final / Resolution: 2.4→19.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 23 144 4379
Biso mean--69.52 64.7 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024338
X-RAY DIFFRACTIONf_angle_d0.4175870
X-RAY DIFFRACTIONf_chiral_restr0.034631
X-RAY DIFFRACTIONf_plane_restr0.003736
X-RAY DIFFRACTIONf_dihedral_angle_d13.4752566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.47730.39191200.33522642276297
2.4773-2.56570.3411300.30952636276697
2.5657-2.66820.35451470.30412643279097
2.6682-2.78930.35951420.28712636277897
2.7893-2.9360.29331400.26962644278496
2.936-3.11930.30031450.26322638278397
3.1193-3.3590.26641270.23732704283197
3.359-3.69510.26381500.20782703285398
3.6951-4.22540.20661320.17542739287197
4.2254-5.30680.19371510.15822799295099
5.3068-19.92540.18191650.16452940310599

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