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- PDB-7w6d: Polyketide cyclase OAC-F24I mutant from Cannabis sativa in comple... -

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Basic information

Entry
Database: PDB / ID: 7w6d
TitlePolyketide cyclase OAC-F24I mutant from Cannabis sativa in complex with olivetolic acid
ComponentsOlivetolic acid cyclase
KeywordsLYASE / olivetolic acid cyclase / polypeptide 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 / Dimeric alpha-beta barrel
Similarity search - Domain/homology
2,4-bis(oxidanyl)-6-pentyl-benzoic acid / Olivetolic acid cyclase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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)24,8404
Polymers24,3922
Non-polymers4492
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-10 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.795, 39.431, 43.412
Angle α, β, γ (deg.)70.379, 75.480, 67.777
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 / Mutation: F24I
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-4MX / 2,4-bis(oxidanyl)-6-pentyl-benzoic acid


Mass: 224.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES-NaOH pH 6.5, 30% PEG3350, 1.2% 1,3-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.54→40.48 Å / Num. obs: 51358 / % possible obs: 95.4 % / Redundancy: 4 % / Biso Wilson estimate: 13.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 7 / Num. unique obs: 1259 / CC1/2: 0.975 / Rrim(I) all: 0.2 / % possible all: 90.6

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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: 1.54→40.48 Å / SU ML: 0.1308 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 17.3014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.176 2429 4.73 %
Rwork0.1519 48929 -
obs0.153 51358 92.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.27 Å2
Refinement stepCycle: LAST / Resolution: 1.54→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 247 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062041
X-RAY DIFFRACTIONf_angle_d0.9182802
X-RAY DIFFRACTIONf_chiral_restr0.0614298
X-RAY DIFFRACTIONf_plane_restr0.0057359
X-RAY DIFFRACTIONf_dihedral_angle_d21.5531753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.17411370.19712787X-RAY DIFFRACTION89.09
1.57-1.610.23561270.19332877X-RAY DIFFRACTION93.12
1.61-1.640.21581160.18392985X-RAY DIFFRACTION92.9
1.64-1.680.22631330.1872873X-RAY DIFFRACTION93.07
1.68-1.730.17961520.18042933X-RAY DIFFRACTION93.15
1.73-1.780.20441660.18182833X-RAY DIFFRACTION93.08
1.78-1.840.22441360.17612950X-RAY DIFFRACTION93.97
1.84-1.90.18111410.17332826X-RAY DIFFRACTION91.63
1.9-1.980.21511370.16222924X-RAY DIFFRACTION93.55
1.98-2.070.16681560.15392947X-RAY DIFFRACTION93.18
2.07-2.180.18351490.1532891X-RAY DIFFRACTION93.42
2.18-2.320.20031370.15022917X-RAY DIFFRACTION93.62
2.32-2.490.17151710.14822837X-RAY DIFFRACTION92.33
2.49-2.750.1551520.14652806X-RAY DIFFRACTION90.62
2.75-3.140.1711470.14442879X-RAY DIFFRACTION92.2
3.14-3.960.17671380.12472842X-RAY DIFFRACTION91.13
3.96-40.480.1371340.1392822X-RAY DIFFRACTION90.95
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)
10.0134748845368-0.02408734337260.03597920852390.0552229437278-0.08394590835530.1231492522070.1589497934230.343967923735-0.04897366054340.217699255898-0.1522144549680.118625121652-0.381991978534-0.2903638811850.001341242325710.133239447566-0.00611653007018-0.01666157713010.161500425545-0.02993438816840.18614240581733.12099225484.861383922996.19739784456
20.508267177855-0.2574076777110.1937449547850.354835413689-0.0983467258370.1194743614220.190990147630.09638383685920.208463989602-0.15890274875-0.0709172255671-0.00443665213650.01159190715080.01104805369380.03777052211770.0598825357486-0.002606142275820.01248732711110.07180165099980.01228030994640.10619767101412.039426536912.303463460710.9316691944
30.4328506318260.263525871514-0.5535755992480.523449834503-0.3480190609740.8999265073140.05305806408-0.0313359065570.1669955536710.1884601932520.000407267720930.0379698035754-0.07961683873270.0272326448190.02595817028590.103320105320.01611373775480.01296985669150.0888435394542-0.01969027145570.08428746410559.3314816117413.203400039322.9045692221
40.790759531518-0.363614895309-0.3188746521990.9844311890160.1332577883291.14444711206-0.204012923938-0.198050743145-0.01480208710370.0956992205029-0.0838786658782-0.3152306608630.3233987707480.440046622757-0.2414946449840.1507054466130.07006608474970.003498040927290.1678504713360.03150369996880.064535318837721.9816888922.1774638747419.3113728765
50.3262017802440.219271842282-0.403888748730.45621354803-0.2418510299751.081859687420.1413168890750.148320220040.03303445840760.141195650689-0.005343691783880.28190373021-0.2119786954960.04403299638010.03295064466090.09976988635720.01328871721710.01246745476810.0847114480994-0.009625255298020.25091955380910.593271330420.894006288210.3640297149
60.3173845536880.325892374983-0.1057375874380.2757750070090.008657710535940.1325515009230.103146822275-0.0700824434340.0425793838035-0.159711147761-0.102365171261-0.004574247253420.005106168672970.0829195326708-0.001863423859510.07436922518220.01796308316180.007966344277360.0881901382610.006947395143150.10720470177319.114274940210.282934073712.1126109125
70.578396944776-0.0620473138831-0.1420836058850.78307376170.1136485381260.657779597677-0.04606432758090.0181397059870.032093812938-0.0544495487053-0.009456294674860.03422732966170.1422716818670.00712714266706-0.04242161627350.05577490124990.00632372969793-0.01004429227780.05703315151840.002342591294850.069745171081612.07764108524.934644532212.4652533161
80.289037271799-0.26288489684-0.3740099887550.726763479254-0.1352610009880.392942423967-0.008286693696420.07174281811010.02185089272810.01713819382830.08746890919010.1071267340990.08610607087850.1233045645120.007233430919810.0730728884185-0.0187863320279-0.0111021523580.09004249447850.02001518742890.092783600696815.930297086819.0388750969-0.270098781756
90.1447175629930.0284845402708-0.3057179264550.849776503305-0.2462358789470.6922997836740.04507790753620.0450739354495-0.0845805507438-0.1081502601890.1915772703-0.4048039367350.002625631569360.2407955656360.0341149163740.127436173986-0.00655518644013-0.005184800183530.111838413068-0.02004369577150.11099023991423.880155253222.0897527901-7.87324125147
100.1892269262640.0703349437137-0.2185577235570.265801321613-0.1818009338660.15881698582-0.068919381880.0181071717170.0258463210793-0.0608127730980.0370773740234-0.03997034522080.0915894884146-0.1165564390340.0004530115913120.0910217424088-0.0109070521719-0.01352875616840.08117051234780.002738404489240.10933084093713.57416309568.741663955030.174675353941
110.8764147180740.3493765967650.238742839841.10167323546-0.06457175308420.5939712390610.04214757120220.002598107871290.00171384084-0.0299274417395-0.01012167710170.0321333837121-0.088285765481-0.0459843268370.02745414443570.0650865441177-0.009830891215780.007764458925370.07874969486530.004009422170610.053720903355916.990713850725.6499469918-0.487803917314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 2 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 11 )
3X-RAY DIFFRACTION3chain 'A' and (resid 12 through 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 38 )
5X-RAY DIFFRACTION5chain 'A' and (resid 39 through 56 )
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 65 )
7X-RAY DIFFRACTION7chain 'A' and (resid 66 through 101 )
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 16 )
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 39 )
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 56 )
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 101 )

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