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- PDB-5b0g: Polyketide cyclase OAC from Cannabis sativa, H78S mutant -

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Basic information

Entry
Database: PDB / ID: 5b0g
TitlePolyketide cyclase OAC from Cannabis sativa, H78S 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: 1.4 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


Theoretical massNumber of molelcules
Total (without water)12,1791
Polymers12,1791
Non-polymers00
Water2,792155
1
A: Olivetolic acid cyclase

A: Olivetolic acid cyclase


Theoretical massNumber of molelcules
Total (without water)24,3582
Polymers24,3582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2640 Å2
ΔGint-13 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.000, 32.690, 36.620
Angle α, β, γ (deg.)90.000, 108.250, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

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Components

#1: Protein Olivetolic acid cyclase


Mass: 12178.941 Da / Num. of mol.: 1 / Mutation: H78S
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.: 155 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.5, 30% (w/v) PEG4000

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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: Dec 12, 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: 1.4→50 Å / Num. obs: 18918 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 25.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 9.1 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.594
Highest resolutionLowest resolution
Rotation40.36 Å1.54 Å

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Processing

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

5b08


Resolution: 1.4→40.362 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 946 5 %Random selection
Rwork0.1768 17972 --
obs0.1779 18918 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.68 Å2 / Biso mean: 15.1684 Å2 / Biso min: 5.26 Å2
Refinement stepCycle: final / Resolution: 1.4→40.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 0 155 994
Biso mean---24.42 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009861
X-RAY DIFFRACTIONf_angle_d1.1621166
X-RAY DIFFRACTIONf_chiral_restr0.069128
X-RAY DIFFRACTIONf_plane_restr0.005145
X-RAY DIFFRACTIONf_dihedral_angle_d18.855314
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 (%)
1.4001-1.47390.26541340.20052557269199
1.4739-1.56620.20621340.182125362670100
1.5662-1.68720.21311340.185925572691100
1.6872-1.8570.20141340.182125502684100
1.857-2.12570.19931360.162825732709100
2.1257-2.6780.1651370.173725972734100
2.678-40.3790.20911370.17642602273998
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)
10.1625-0.04690.02560.12060.14010.18980.04720.01320.0394-0.03910.0269-0.0607-0.0732-0.093-00.1149-0.00580.00340.09360.00060.08525.302-0.92773.5144
20.4174-0.23140.03060.1424-0.00180.53510.0174-0.03370.008-0.02170.0280.14110.0861-0.0012-00.0749-0.0092-0.0070.0803-0.00490.07596.6373-0.208316.4422
30.0150.00380.01310.00040.00840.02690.01120.1140.2404-0.09560.0146-0.0177-0.04130.016300.1181-0.0265-0.00160.13340.0060.110915.636310.63345.7313
40.0709-0.01990.02050.07020.07140.0919-0.11760.01170.0813-0.23180.236-0.02950.14330.0038-00.101-0.01910.00380.1134-0.01040.12051.66765.21148.4028
51.575-0.6708-0.04270.3476-0.30451.358-0.0750.1787-0.8842-0.1486-0.01430.26420.5089-0.1940.01160.1781-0.02450.01310.127-0.02980.2173-6.6035-9.12846.0437
60.1178-0.08980.0160.14890.11040.1566-0.0340.13060.2495-0.04050.1687-0.0378-0.10060.03080.00040.1002-0.02370.00180.1319-0.00550.11887.95095.36291.3657
70.43810.10040.22690.09160.24640.6257-0.03930.0486-0.0124-0.02890.0439-0.01460.02940.027-00.09850.00310.01310.10410.00270.102412.3448-0.74483.9726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 11 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 32 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 38 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 44 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 45 through 56 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 66 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 67 through 101 )A0

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