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- PDB-5b0c: Polyketide cyclase OAC from Cannabis sativa, Y27F mutant -

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Basic information

Entry
Database: PDB / ID: 5b0c
TitlePolyketide cyclase OAC from Cannabis sativa, Y27F 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: 1.602 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


Theoretical massNumber of molelcules
Total (without water)24,4282
Polymers24,4282
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-15 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.920, 30.320, 36.740
Angle α, β, γ (deg.)90.000, 108.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid ARO
21chain B and segid BRO

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AROA0
211chain B and segid BROB0

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Components

#1: Protein Olivetolic acid cyclase


Mass: 12214.011 Da / Num. of mol.: 2 / Mutation: Y27F
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 34.84 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 100mM Sodium HEPES, pH 7.5, 25%(w/v) PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 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: 1.6→50 Å / Num. obs: 23862 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 42.3
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 13 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.828
Highest resolutionLowest resolution
Rotation36.49 Å1.82 Å

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Processing

Software
NameVersionClassification
MOLREPphasing
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: 1.602→36.496 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1194 5 %Random selection
Rwork0.1927 22672 --
obs0.1946 23862 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.71 Å2 / Biso mean: 15.6263 Å2 / Biso min: 5.36 Å2
Refinement stepCycle: final / Resolution: 1.602→36.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 0 229 1913
Biso mean---21.73 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071730
X-RAY DIFFRACTIONf_angle_d1.1492342
X-RAY DIFFRACTIONf_chiral_restr0.053256
X-RAY DIFFRACTIONf_plane_restr0.006292
X-RAY DIFFRACTIONf_dihedral_angle_d14.058628
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A940X-RAY DIFFRACTION6.314TORSIONAL
12B940X-RAY DIFFRACTION6.314TORSIONAL
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 (%)
1.6017-1.66580.21841290.18052444257398
1.6658-1.74160.24511310.186624982629100
1.7416-1.83340.2641340.197625292663100
1.8334-1.94830.25251310.194424992630100
1.9483-2.09870.22161320.177925102642100
2.0987-2.30990.24671340.194525352669100
2.3099-2.64410.21591330.203925452678100
2.6441-3.33090.23631350.200225512686100
3.3309-36.50550.21341350.18822561269697

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