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- PDB-2ong: Crystal Structure of of limonene synthase with 2-fluorogeranyl di... -

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Basic information

Entry
Database: PDB / ID: 2ong
TitleCrystal Structure of of limonene synthase with 2-fluorogeranyl diphosphate (FGPP).
Components4S-limonene synthase
KeywordsLYASE / monoterpene synthase / monoterpene cyclase / geranyl diphosphate / 2 fluorogeranyl diphosphate / linalyl diphosphate / 2-fluorolinalyl diphosphate
Function / homology
Function and homology information


diterpenoid biosynthetic process / terpene synthase activity / 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
Chem-FPG / : / 4S-limonene synthase
Similarity search - Component
Biological speciesMentha spicata (spearmint)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHyatt, D.C. / Youn, B. / Croteau, R. / Kang, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of limonene synthase, a simple model for terpenoid cyclase catalysis.
Authors: Hyatt, D.C. / Youn, B. / Zhao, Y. / Santhamma, B. / Coates, R.M. / Croteau, R.B. / Kang, C.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4S-limonene synthase
B: 4S-limonene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,62914
Polymers127,7902
Non-polymers1,83912
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.48, 200.48, 123.41
Angle α, β, γ (deg.)90, 90, 90
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a dimer which has two molecules in the asymmetric unit.

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Components

#1: Protein 4S-limonene synthase


Mass: 63895.074 Da / Num. of mol.: 2 / Mutation: E57M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mentha spicata (spearmint) / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / References: UniProt: Q40322
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FPG / (1S)-1-[(1R)-1-FLUOROETHYL]-1,5-DIMETHYLHEXYL TRIHYDROGEN DIPHOSPHATE


Mass: 336.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H23FO7P2
#4: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.85 Å3/Da / Density % sol: 74.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 300 mM BisTris, pH 6.8, 7.0% polyethylene glycol 8000, 25 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.07812 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28338 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Rsym value: 0.062
Reflection shellResolution: 2.7→2.81 Å / Rsym value: 0.164

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data collection
AMoREphasing
X-PLOR3.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N24

1n24


Resolution: 2.7→10 Å / Cross valid method: THROUGHOUT / σ(I): 2
RfactorNum. reflectionSelection details
Rfree0.241 -RANDOM
Rwork0.208 --
obs-28338 -
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8986 0 102 93 9181

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