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- PDB-5b09: Polyketide cyclase OAC from Cannabis sativa bound with Olivetolic acid -

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Basic information

Entry
Database: PDB / ID: 5b09
TitlePolyketide cyclase OAC from Cannabis sativa bound with Olivetolic acid
ComponentsOlivetolic acid cyclase
KeywordsLYASE / Cannabis sativa / plant polyketide cyclase
Function / homology
Function and homology information


olivetolic acid cyclase / olivetolic acid biosynthetic process / cannabinoid biosynthetic process / cyclase activity / terpenoid biosynthetic process / lyase activity / metal ion binding / cytoplasm
Similarity search - Function
Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,4-bis(oxidanyl)-6-pentyl-benzoic acid / Olivetolic acid cyclase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsYang, X. / Matsui, T. / Mori, T. / Abe, I. / Morita, H.
CitationJournal: Febs J. / Year: 2016
Title: Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa
Authors: Yang, X. / Matsui, T. / Kodama, T. / Mori, T. / Zhou, X. / Taura, F. / Noguchi, H. / Abe, I. / Morita, H.
History
DepositionOct 28, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Olivetolic acid cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4542
Polymers12,2301
Non-polymers2241
Water1,00956
1
A: Olivetolic acid cyclase
hetero molecules

A: Olivetolic acid cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9094
Polymers24,4602
Non-polymers4492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2860 Å2
ΔGint-9 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.480, 30.440, 36.890
Angle α, β, γ (deg.)90.000, 108.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Olivetolic acid cyclase /


Mass: 12230.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Gene: OAC / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: I6WU39, olivetolic acid cyclase
#2: Chemical ChemComp-4MX / 2,4-bis(oxidanyl)-6-pentyl-benzoic acid


Mass: 224.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 100mM Tris - HCl pH 8.8, 25%(w/v) PEG6000, 50mM olivetolic acid, 5%(v/v) methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2014
RadiationMonochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 10098 / % possible obs: 98.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 27.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.1 / % possible all: 92.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.96 Å32.11 Å
Translation2.96 Å32.11 Å

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Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B08

5b08


Resolution: 1.7→32.112 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 505 5 %Random selection
Rwork0.1968 9589 --
obs0.1981 10094 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.58 Å2 / Biso mean: 24.0696 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 1.7→32.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 16 56 883
Biso mean--31.6 30.5 -
Num. residues----96
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01849
X-RAY DIFFRACTIONf_angle_d1.1561149
X-RAY DIFFRACTIONf_chiral_restr0.061124
X-RAY DIFFRACTIONf_plane_restr0.005141
X-RAY DIFFRACTIONf_dihedral_angle_d14.538305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6998-1.87090.2651190.21792271239095
1.8709-2.14160.2431270.190324152542100
2.1416-2.69790.2391280.2124152543100
2.6979-32.11740.20431310.189724882619100

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