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- PDB-5b0a: Polyketide cyclase OAC from Cannabis sativa, H5Q mutant -

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Basic information

Entry
Database: PDB / ID: 5b0a
TitlePolyketide cyclase OAC from Cannabis sativa, H5Q 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _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

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Assembly

Deposited unit
A: Olivetolic acid cyclase
B: Olivetolic acid cyclase


Theoretical massNumber of molelcules
Total (without water)24,4402
Polymers24,4402
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-11 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.800, 30.490, 81.530
Angle α, β, γ (deg.)90.000, 95.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Olivetolic acid cyclase


Mass: 12219.993 Da / Num. of mol.: 2 / Mutation: H5Q
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.: 51 / 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: 1.86 Å3/Da / Density % sol: 33.97 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 100mM Sodium acetate, 25%(w/v) PEG4000, 8%(v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 10898 / % possible obs: 95.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 31.9
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 13 / % possible all: 91.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å34.65 Å
Translation2.1 Å34.65 Å

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Processing

Software
NameVersionClassification
PHENIX1.10_2152refinement
PHASER2.6.0phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B08

5b08


Resolution: 2.1→34.654 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 521 5.01 %Random selection
Rwork0.2221 9885 --
obs0.2247 10406 95.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.31 Å2 / Biso mean: 27.8493 Å2 / Biso min: 13.02 Å2
Refinement stepCycle: final / Resolution: 2.1→34.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 0 51 1655
Biso mean---28 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111645
X-RAY DIFFRACTIONf_angle_d1.1232224
X-RAY DIFFRACTIONf_chiral_restr0.07244
X-RAY DIFFRACTIONf_plane_restr0.007274
X-RAY DIFFRACTIONf_dihedral_angle_d17.731596
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 (%)
2.0957-2.30660.3211240.24492354247892
2.3066-2.64020.32791300.25372473260396
2.6402-3.3260.29061310.23612485261697
3.326-34.65870.22991360.19612573270997

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