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- PDB-5b0b: Polyketide cyclase OAC from Cannabis sativa, I7F mutant -

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Basic information

Entry
Database: PDB / ID: 5b0b
TitlePolyketide cyclase OAC from Cannabis sativa, I7F 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
ACETATE ION / Olivetolic acid cyclase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.187 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
C: Olivetolic acid cyclase
D: Olivetolic acid cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2928
Polymers49,0564
Non-polymers2364
Water3,081171
1
A: Olivetolic acid cyclase
C: Olivetolic acid cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6464
Polymers24,5282
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-14 kcal/mol
Surface area9500 Å2
MethodPISA
2
B: Olivetolic acid cyclase
D: Olivetolic acid cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6464
Polymers24,5282
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-18 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.400, 45.253, 94.408
Angle α, β, γ (deg.)90.000, 96.300, 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
31chain C and segid CRO
41chain D and segid DRO

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AROA0
211chain B and segid BROB0
311chain C and segid CROC0
411chain D and segid DROD0

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Components

#1: Protein
Olivetolic acid cyclase


Mass: 12264.027 Da / Num. of mol.: 4 / Mutation: I7F
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 35.01 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 100 mM Sodium acetate, pH 4.7, 25% (w/v) PEG2000MME

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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 9, 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: 2.18→50 Å / Num. obs: 19023 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.77 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Χ2: 1.464 / Net I/av σ(I): 21.5 / Net I/σ(I): 10.5 / Num. measured all: 70778
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.18-2.263.60.29618280.9080.1790.3461.33296
2.26-2.353.80.25518540.9340.1520.2981.3899.3
2.35-2.463.80.22818860.9540.1360.2651.39599.6
2.46-2.583.80.18119130.970.1080.2111.34299.6
2.58-2.753.80.14718940.980.0880.1711.39999.7
2.75-2.963.80.11618810.9850.0690.1351.46299.7
2.96-3.263.70.07719290.9940.0460.091.45399.9
3.26-3.733.70.05319130.9970.0320.0621.523100
3.73-4.73.70.0419360.9980.0240.0471.637100
4.7-503.60.03819890.9980.0230.0451.70399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.583
Highest resolutionLowest resolution
Rotation43.14 Å2.41 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B08

5b08


Resolution: 2.187→43.138 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 917 4.82 %Random selection
Rwork0.2015 18094 --
obs0.2041 19011 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.24 Å2 / Biso mean: 25.547 Å2 / Biso min: 13.71 Å2
Refinement stepCycle: final / Resolution: 2.187→43.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 16 171 3331
Biso mean--23.4 31.68 -
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013248
X-RAY DIFFRACTIONf_angle_d1.2894396
X-RAY DIFFRACTIONf_chiral_restr0.064476
X-RAY DIFFRACTIONf_plane_restr0.007540
X-RAY DIFFRACTIONf_dihedral_angle_d15.3131148
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1790X-RAY DIFFRACTION11.43TORSIONAL
12B1790X-RAY DIFFRACTION11.43TORSIONAL
13C1790X-RAY DIFFRACTION11.43TORSIONAL
14D1790X-RAY DIFFRACTION11.43TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1875-2.30280.31631280.22122531265998
2.3028-2.44710.32721280.226425432671100
2.4471-2.6360.29861170.226825932710100
2.636-2.90120.30541360.22625712707100
2.9012-3.32090.27881390.219425752714100
3.3209-4.18340.20051230.179126282751100
4.1834-43.14650.21491460.179226532799100

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