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- PDB-6onm: Crystal Structure of (+)-Limonene Synthase Complexed with 8,9-Dif... -

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Basic information

Entry
Database: PDB / ID: 6onm
TitleCrystal Structure of (+)-Limonene Synthase Complexed with 8,9-Difluorolinalyl Diphosphate
Components(+)-limonene synthase
KeywordsLYASE / Terpene synthase / enantiomer / terpene synthase fold / monoterpene / fluoro analog / metal binding
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
: / Chem-MWG / (R)-limonene synthase 1, chloroplastic
Similarity search - Component
Biological speciesCitrus sinensis (sweet orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsPrem Kumar, R. / Morehouse, B.R. / Yu, Q. / Oprian, D.D.
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Direct Evidence of an Enzyme-Generated LPP Intermediate in (+)-Limonene Synthase Using a Fluorinated GPP Substrate Analog.
Authors: Morehouse, B.R. / Kumar, R.P. / Matos, J.O. / Yu, Q. / Bannister, A. / Malik, K. / Temme, J.S. / Krauss, I.J. / Oprian, D.D.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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_seq_id / _struct_conn.ptnr2_label_asym_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)70,9565
Polymers70,4411
Non-polymers5154
Water41423
1
A: (+)-limonene synthase
hetero molecules

A: (+)-limonene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,91210
Polymers140,8822
Non-polymers1,0308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2950 Å2
ΔGint-48 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.810, 85.810, 217.620
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) / Variant (production host): BL21-CodonPlus(DE3) / References: UniProt: A0A1C9J6A7, (R)-limonene synthase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MWG / (3R)-8-fluoro-7-(fluoromethyl)-3-methylocta-1,6-dien-3-yl trihydrogen diphosphate


Mass: 350.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18F2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2017 / 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: 2.7→20 Å / Num. obs: 23172 / % possible obs: 99.8 % / Redundancy: 26.7 % / Biso Wilson estimate: 70.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Net I/σ(I): 15.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 27.8 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3302 / CC1/2: 0.822 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.13rc1_2954refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uv0

5uv0


Resolution: 2.7→19.957 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2406 1212 5.26 %
Rwork0.2057 --
obs0.2076 23047 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.04 Å2 / Biso mean: 71.4766 Å2 / Biso min: 38.59 Å2
Refinement stepCycle: final / Resolution: 2.7→19.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 24 23 4139
Biso mean--77.93 62 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.80790.41211200.327623742494100
2.8079-2.93530.31241200.294523832503100
2.9353-3.08950.30671250.291823952520100
3.0895-3.28230.34181290.282823932522100
3.2823-3.53440.28331430.235923872530100
3.5344-3.88780.26171540.213424002554100
3.8878-4.44490.18951390.17812421256099
4.4449-5.57980.24341350.174224742609100
5.5798-19.95760.17741470.170826082755100

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