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- PDB-7ffg: Diarylpentanoid-producing polyketide synthase (N199F mutant) -

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Basic information

Entry
Database: PDB / ID: 7ffg
TitleDiarylpentanoid-producing polyketide synthase (N199F mutant)
ComponentsType III polyketide synthase
KeywordsTRANSFERASE / diarylpentanoid / type-III polyketide synthase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / endoplasmic reticulum
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Type III polyketide synthase
Similarity search - Component
Biological speciesAquilaria sinensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMorita, H. / Wong, C.P. / Liu, Q. / Kodama, T. / Lee, Y. / Nakashima, Y.
CitationJournal: Nat Commun / Year: 2022
Title: Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood.
Authors: Wang, X.H. / Gao, B.W. / Nakashima, Y. / Mori, T. / Zhang, Z.X. / Kodama, T. / Lee, Y.E. / Zhang, Z.K. / Wong, C.P. / Liu, Q.Q. / Qi, B.W. / Wang, J. / Li, J. / Liu, X. / Abe, I. / Morita, H. ...Authors: Wang, X.H. / Gao, B.W. / Nakashima, Y. / Mori, T. / Zhang, Z.X. / Kodama, T. / Lee, Y.E. / Zhang, Z.K. / Wong, C.P. / Liu, Q.Q. / Qi, B.W. / Wang, J. / Li, J. / Liu, X. / Abe, I. / Morita, H. / Tu, P.F. / Shi, S.P.
History
DepositionJul 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Type III polyketide synthase
B: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,7572
Polymers93,7572
Non-polymers00
Water2,324129
1
A: Type III polyketide synthase

A: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,7572
Polymers93,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5250 Å2
ΔGint-17 kcal/mol
Surface area26090 Å2
MethodPISA
2
B: Type III polyketide synthase

B: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,7572
Polymers93,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5170 Å2
ΔGint-18 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.617, 65.136, 108.019
Angle α, β, γ (deg.)90.000, 128.114, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Type III polyketide synthase


Mass: 46878.672 Da / Num. of mol.: 2 / Mutation: N199F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquilaria sinensis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A385MEG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl, pH 8.5, 25% PEG 8000, 0.3M KF, 4% butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.49 Å / Num. obs: 35813 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 42.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3480 / CC1/2: 0.937 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FFA

7ffa


Resolution: 2.3→41.7 Å / SU ML: 0.2512 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2214 1720 4.81 %
Rwork0.1874 34062 -
obs0.189 35782 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5894 0 0 129 6023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046018
X-RAY DIFFRACTIONf_angle_d0.74468176
X-RAY DIFFRACTIONf_chiral_restr0.0477948
X-RAY DIFFRACTIONf_plane_restr0.00471048
X-RAY DIFFRACTIONf_dihedral_angle_d19.24532192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.27341410.25372781X-RAY DIFFRACTION99.69
2.37-2.440.26241400.22842856X-RAY DIFFRACTION99.9
2.44-2.530.31061440.23242808X-RAY DIFFRACTION99.93
2.53-2.630.3191520.23412789X-RAY DIFFRACTION99.86
2.63-2.750.27441220.23632863X-RAY DIFFRACTION99.83
2.75-2.90.2941450.24042801X-RAY DIFFRACTION99.93
2.9-3.080.25441470.22712858X-RAY DIFFRACTION99.93
3.08-3.320.25631670.21012804X-RAY DIFFRACTION99.9
3.32-3.650.24481380.18662849X-RAY DIFFRACTION99.57
3.65-4.180.17841680.16812832X-RAY DIFFRACTION99.97
4.18-5.260.16111240.14552876X-RAY DIFFRACTION100
5.26-41.70.18121320.15892945X-RAY DIFFRACTION99.61
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)
11.76221208221-0.156976965663-0.2503219384120.496025749723-0.7397395810342.94087160651-0.151772392796-0.0780009449677-0.658329776830.048785051728-0.01268752274040.01195449722340.8444879274620.2088742279930.1282412677790.5920553751270.06931430074960.1154176325960.337844188861-0.0886015348950.465606227694-25.9693681541-33.011805026834.209855864
23.1228356160.927379941279-0.4934610016232.82924038661.568701422822.510258902380.218573671692-0.2478813659660.981873704183-0.07277637528740.183190778361-0.537757666597-0.8654301947130.831449685385-0.4187022451530.50437171581-0.1976563167790.1309133179720.550039965305-0.1040787820.667513798416-12.45329827923.3940597697535.4598236714
33.036997544640.52113632657-1.574284048723.96890636139-0.5261707818362.25643171149-0.09046945882440.208999514280.013950497559-0.2195221378820.1506573126930.008191486397150.279574553573-0.0201161449549-0.05774133175040.249549608460.0055305814541-0.04582205725690.247623662464-0.006257454470080.163620038421-28.5772651224-17.018030523933.2649975152
43.291679240990.321949411455-1.472777025990.959344824093-1.405261907422.5332694568-0.128056349158-0.152484288046-0.4354228220850.2007790676050.0902849892529-0.2501440922550.5644841659450.3604007328910.02823045211170.4010126421080.0946209744193-0.01355610517780.350341493512-0.003381730735620.255603680343-19.8039029767-24.407085532836.8654047679
53.78983008949-0.7561211982331.407961191887.54479051544-3.176846999015.66974799019-0.0114020985917-1.200353715610.7235590542081.284062204860.0172880409966-0.674991360818-0.7631817132220.5213517551-0.0623835144430.582035556275-0.0561360964395-0.04023310664210.631448515803-0.1539221421730.49998243215-21.7491155164-6.6153528041852.8657182705
62.612969965260.413451882122-0.06885040582120.536230213948-1.396280079814.22392434316-0.257909130126-1.12080231726-0.4527442644180.607987508727-0.070245099745-0.8653069095670.6329250967571.071760248380.30541081850.5528771862240.261240757161-0.06814197296790.9917879388590.1019536613850.667357968548-9.56947573363-26.778266380850.129105678
72.142403559740.2087964452781.72302605813.80547367387-1.316708452062.78989173913-0.055429204381-0.504922942457-0.2936510556560.00895524328962-0.0622690528567-0.9862808868630.429744063581.244491148350.1048943025680.3216629603120.1261459554070.03748877297540.7319430472820.01317068966250.496592080245-7.23547099023-20.679069408538.5002817791
83.62423933097-0.851776509199-1.751082513924.480935706341.50981536923.99557641282-0.272372317029-0.495749186033-0.511512827725-0.2417970413740.241838295792-0.6551708078040.6356712243251.040876139440.06119443557820.5225488954080.2339187363430.04430854179420.5967847729490.04028732346650.456673385715-13.1677713573-29.491988389841.3858731047
93.86731781705-0.242373566767-0.4689010453812.72989067145-0.004018336979933.21196132183-0.00245822197873-0.02191204837890.5875134965820.03477720309170.1788695026470.302124923766-0.442041128287-0.600203525957-0.1349892558660.3330380937030.05901048260030.07756909745120.3955507429650.04597393953070.374983720399-14.36561780962.869526440035.20711037028
104.25492487736-0.499207031931-0.6473847355252.43969638360.6405579369493.79955385793-0.0396925306610.8168038065190.00637354160108-0.5442236437890.09651647087070.477925950855-0.00895275232677-0.845561527832-0.07067693896010.344436044853-0.0665283548778-0.02225791510550.5525063254410.04840393545710.38830111088-16.262524211-7.7658111874-6.08161975257
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 31 )AA7 - 311 - 25
22chain 'A' and (resid 32 through 92 )AA32 - 9226 - 86
33chain 'A' and (resid 93 through 208 )AA93 - 20887 - 202
44chain 'A' and (resid 209 through 248 )AA209 - 248203 - 242
55chain 'A' and (resid 249 through 272 )AA249 - 272243 - 266
66chain 'A' and (resid 273 through 308 )AA273 - 308267 - 302
77chain 'A' and (resid 309 through 358 )AA309 - 358303 - 352
88chain 'A' and (resid 359 through 391 )AA359 - 391353 - 385
99chain 'B' and (resid 7 through 156 )BB7 - 1561 - 150
1010chain 'B' and (resid 157 through 391 )BB157 - 391151 - 385

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