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- PDB-5b0f: Polyketide cyclase OAC from Cannabis sativa, Y72F mutant -

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Basic information

Entry
Database: PDB / ID: 5b0f
TitlePolyketide cyclase OAC from Cannabis sativa, Y72F mutant
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 / pollen tube adhesion / 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
Olivetolic acid cyclase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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
B: Olivetolic acid cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5203
Polymers24,4282
Non-polymers921
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-17 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.810, 63.590, 46.590
Angle α, β, γ (deg.)90.000, 108.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Olivetolic acid cyclase


Mass: 12214.011 Da / Num. of mol.: 2 / Mutation: Y72F
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 300 mM tris - Sodium citrate, 33% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2014
RadiationMonochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 25752 / % possible obs: 98 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 3 / % possible all: 96.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.598
Highest resolutionLowest resolution
Rotation44.23 Å1.84 Å

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Processing

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

5b08


Resolution: 1.6→44.226 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1288 5 %Random selection
Rwork0.1754 24463 --
obs0.1777 25751 98.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.36 Å2 / Biso mean: 27.2128 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: final / Resolution: 1.6→44.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 6 136 1826
Biso mean--23.51 33.52 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061735
X-RAY DIFFRACTIONf_angle_d1.0052347
X-RAY DIFFRACTIONf_chiral_restr0.046257
X-RAY DIFFRACTIONf_plane_restr0.004292
X-RAY DIFFRACTIONf_dihedral_angle_d14.984630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5999-1.6640.3381390.25932646278597
1.664-1.73970.25011430.23652709285298
1.7397-1.83150.27771410.22262686282798
1.8315-1.94620.23751430.19812716285998
1.9462-2.09650.24221430.17552724286799
2.0965-2.30740.21521440.17872728287299
2.3074-2.64130.21411440.17982743288799
2.6413-3.32760.23571470.169827902937100
3.3276-44.2430.18811440.14742721286597
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.685-1.0473-0.46281.0418-0.55891.98020.2437-0.31020.32190.0516-0.23110.0206-0.31850.0023-00.2507-0.06890.02620.1807-0.01650.20555.8213.456816.2656
20.8602-0.8963-0.33881.00010.41211.4717-0.0033-0.2953-0.05980.09420.0210.05510.00730.1333-00.1959-0.0077-0.01290.21830.01460.18985.297-1.635625.635
30.2058-0.21540.11320.2799-0.30950.7751-0.06860.0997-0.2510.16630.21460.15550.2396-0.363300.292-0.0540.00450.27320.03120.29851.7204-8.942418.4426
41.7716-1.66571.42691.7966-0.97931.72440.620.70410.8524-1.037-0.3527-0.4179-0.24030.9081-0.00810.3302-0.04340.06280.28780.06130.359113.99074.95347.3704
50.3752-0.4140.2720.494-0.1920.5293-0.06710.2757-0.4594-0.06650.18440.0430.1011-0.25100.227-0.0454-0.01350.20790.00950.2426-0.6012-6.631414.6819
61.5777-0.3101-0.41290.5006-0.42022.31120.0131-0.01610.0636-0.04440.1095-0.0318-0.2012-0.400500.21760.01130.01110.23390.02610.2272-3.76691.048716.7682
72.35850.0021-1.69970.86770.87543.1252-0.11490.2177-0.09350.10580.1762-0.05320.1302-0.2907-0.00010.186-0.028-0.02290.202-0.010.194.3064-7.5952-4.0923
80.1008-0.1803-0.04380.34450.05110.19950.19710.09910.29980.1302-0.14280.0086-0.3763-0.379300.2780.06540.00550.240.04370.2546-4.09145.77974.8358
90.61360.6163-0.39351.01580.32171.2083-0.1816-0.1976-0.35250.31540.1324-0.35560.26190.393600.28670.0735-0.03940.31710.01060.334314.3091-11.38492.7582
101.7304-0.24150.2851.08470.20650.8192-0.01560.07010.11010.06430.1007-0.1859-0.2055-0.01900.1902-0.00040.01050.1831-0.00530.241510.7071-2.727-0.733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 33 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 44 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 56 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 65 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 101 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 44 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 56 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 75 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 101 )B0

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