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- PDB-7w6f: Polyketide cyclase OAC-F24I mutant from Cannabis sativa in comple... -

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Basic information

Entry
Database: PDB / ID: 7w6f
TitlePolyketide cyclase OAC-F24I mutant from Cannabis sativa in complex with 6-nonylresorcylic acid
ComponentsOlivetolic acid cyclase
KeywordsLYASE / olivetolic acid cyclase / polypeptide cyclase
Function / homology
Function and homology information


olivetolic acid cyclase / olivetolic acid biosynthetic process / pollen tube adhesion / cannabinoid biosynthetic process / 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 / Dimeric alpha-beta barrel
Similarity search - Domain/homology
2-nonyl-4,6-bis(oxidanyl)benzoic acid / Olivetolic acid cyclase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsNakashima, Y. / Lee, Y.E. / Morita, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Org.Lett. / Year: 2022
Title: Dual Engineering of Olivetolic Acid Cyclase and Tetraketide Synthase to Generate Longer Alkyl-Chain Olivetolic Acid Analogs.
Authors: Lee, Y.E. / Nakashima, Y. / Kodama, T. / Chen, X. / Morita, H.
History
DepositionDec 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)25,0455
Polymers24,3922
Non-polymers6533
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-11 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.849, 39.317, 43.005
Angle α, β, γ (deg.)70.909, 76.378, 67.383
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Olivetolic acid cyclase


Mass: 12195.995 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Gene: OAC / Production host: Escherichia coli M15 (bacteria) / References: UniProt: I6WU39, olivetolic acid cyclase
#2: Chemical ChemComp-8I6 / 2-nonyl-4,6-bis(oxidanyl)benzoic acid


Mass: 280.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES-NaOH pH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.58→40.32 Å / Num. obs: 47509 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.067 / Net I/σ(I): 9.4
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1188 / CC1/2: 0.884 / Rrim(I) all: 0.43 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B08

5b08


Resolution: 1.58→40.32 Å / SU ML: 0.1476 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 17.0396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1686 2320 4.88 %
Rwork0.1476 45189 -
obs0.1486 47509 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.47 Å2
Refinement stepCycle: LAST / Resolution: 1.58→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 6 260 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641904
X-RAY DIFFRACTIONf_angle_d1.00722595
X-RAY DIFFRACTIONf_chiral_restr0.0586279
X-RAY DIFFRACTIONf_plane_restr0.0065326
X-RAY DIFFRACTIONf_dihedral_angle_d23.1297701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.610.28341190.22822513X-RAY DIFFRACTION89.1
1.61-1.650.27781190.22612652X-RAY DIFFRACTION90.79
1.65-1.690.23231550.21522632X-RAY DIFFRACTION92.47
1.69-1.730.22681380.20482618X-RAY DIFFRACTION92.3
1.73-1.770.19881370.20172684X-RAY DIFFRACTION92.92
1.77-1.830.25071460.18572655X-RAY DIFFRACTION94.18
1.83-1.890.17871510.16452620X-RAY DIFFRACTION92.8
1.89-1.950.1621320.15062692X-RAY DIFFRACTION94.01
1.95-2.030.19431650.14442671X-RAY DIFFRACTION94.03
2.03-2.120.16831280.13912695X-RAY DIFFRACTION94.73
2.12-2.240.19631310.13942713X-RAY DIFFRACTION94.55
2.24-2.380.17011360.13652706X-RAY DIFFRACTION94.04
2.38-2.560.17431330.14012678X-RAY DIFFRACTION94.9
2.56-2.820.16241080.14332748X-RAY DIFFRACTION94.13
2.82-3.220.16181570.13472643X-RAY DIFFRACTION94.02
3.22-4.060.12051400.11942724X-RAY DIFFRACTION94.4
4.06-40.320.13041250.13792545X-RAY DIFFRACTION89.48
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)
10.08598970705040.06767430970710.06293535925240.1189166078240.04148377904710.171095674634-0.0158003494958-0.01003692107640.05799388462950.01671685518590.0588205220403-0.03920667129860.008941618478290.03118498712170.02204546859780.09797563880050.01853040365940.0001648490885690.1063595284530.01206072331580.11918416963312.649285718612.284544664712.420875693
20.07569187732680.0632988504015-0.039999320480.0831985852659-0.03076176457020.0612631995281-0.0578104920375-0.235247005120.1773968120350.1148726334240.137734165578-0.0762027418476-0.02286488336480.02395127126070.007190960851620.1262407164360.0110171595047-0.003207659501680.1112678099910.003134885853460.11033099363811.881996638512.284979016324.3150778305
30.07963379400410.0421821495007-0.1570846985410.0309114409822-0.02124087964110.139318708079-0.0810867617963-0.07123305467720.1165617009130.2704910793120.0719272649976-0.180538690220.005531311743320.1886464653780.009566420256520.1261972452220.0234441649611-0.03022299511020.1326312723350.0119209558480.11452316641320.08464353619.6628447871117.9564026036
40.176926654622-0.0168365160179-0.2915739687080.368538769408-0.0576936737370.493648027015-0.003222751206940.03477854080430.0247534931169-0.0215688508671-0.008113984990950.009148712456770.0526794358952-0.024241905077-0.004664974162250.09438752859870.00779831192304-0.008780070554940.1048876221940.009509833078660.11994629428912.21758359849.345556177811.595725782
50.106176386036-0.064961267328-0.1074071915330.131981061759-0.04849280738990.09856076504930.04538579323980.0473601634702-0.09643197086980.010390852730.0429505328796-0.05076253766210.103852000157-0.03938565907425.72057261426E-50.14345170051-0.0149011649277-0.005862983210620.131183433471-0.0009675105613220.12822549611316.292928992918.9470630512-0.33684461157
60.0579851661046-0.0436410708165-0.109126447410.308011888121-0.008076787250130.2409989127330.0437351054054-0.0229818143397-0.04864346941710.03178502884510.289626983684-0.5057903678030.02691871481450.3390086111660.0237134338940.15050303879-0.0009075175025010.01197721944870.142020870211-0.02672762709430.15439286234624.119701479822.2305138386-8.17569971531
70.133577181817-0.142525082682-0.07496520255350.12159898626-0.1003999774050.0989032078478-0.0945197538956-0.003300222879720.221648454492-0.186925433760.0619856143-0.02074827745970.0312611455059-0.03730389030157.14456682633E-50.110614416194-0.0149326388678-0.005881642598280.1055672378-0.007508143974420.1543642970714.55115936089.897976407630.0726846649289
80.07447771013290.1109646073570.01848588722630.08754372352410.1027060250510.0231561061460.03478015307480.0130891627906-0.04679885753-0.0188375932704-0.0265711952827-0.173994468085-0.0565870264550.0400795750829-0.000638887777550.108519865747-0.02026581727420.001496674013650.093768622954-0.005143302938340.11550208134320.453792653927.94119833732.44875619192
90.1920499693310.122221361212-0.06249410412450.3377964095040.1676690504180.130754005982-0.0217064612047-0.0170927325754-0.0559191562898-0.029428165462-0.0139843925595-0.0396589156137-0.0187813635871-0.0167327073168-0.01199429312460.109371508247-0.0145977342938-0.003415687924790.1360230644580.005170160755550.091332387959514.622363490823.4699526739-2.50856516782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 101 )
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 16 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 38 )
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 75 )
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 101 )

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