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- PDB-7ffc: Diarylpentanoid-producing polyketide synthase (A210E mutant) -

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Basic information

Entry
Database: PDB / ID: 7ffc
TitleDiarylpentanoid-producing polyketide synthase (A210E mutant)
ComponentsType III polyketide synthase
KeywordsTRANSFERASE / diarylpentanoid / type-III polyketide synthase
Function / homologyChalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase-like / Type III polyketide synthase
Function and homology information
Biological speciesAquilaria sinensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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
C: Type III polyketide synthase
D: Type III polyketide synthase
E: Type III polyketide synthase
F: Type III polyketide synthase
G: Type III polyketide synthase
H: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,61023
Polymers375,2298
Non-polymers1,38115
Water7,278404
1
A: Type III polyketide synthase
hetero molecules

E: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0845
Polymers93,8072
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area6240 Å2
ΔGint-20 kcal/mol
Surface area27160 Å2
MethodPISA
2
B: Type III polyketide synthase
F: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9914
Polymers93,8072
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-14 kcal/mol
Surface area27330 Å2
MethodPISA
3
C: Type III polyketide synthase
G: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0845
Polymers93,8072
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-17 kcal/mol
Surface area27140 Å2
MethodPISA
4
D: Type III polyketide synthase
hetero molecules

H: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4529
Polymers93,8072
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7120 Å2
ΔGint-17 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.020, 126.893, 118.166
Angle α, β, γ (deg.)90.000, 99.383, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Type III polyketide synthase


Mass: 46903.633 Da / Num. of mol.: 8 / Mutation: A210E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquilaria sinensis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A385MEG6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl, pH 8.5, 15% PEG 8000, 0.12M 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: Feb 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.61→49.13 Å / Num. obs: 95054 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 33.52 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.141 / Net I/σ(I): 6
Reflection shellResolution: 2.61→2.65 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4146 / CC1/2: 0.759 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FFA

7ffa


Resolution: 2.61→49.13 Å / SU ML: 0.3635 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 31.6757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.269 1996 2.1 %
Rwork0.2188 92846 -
obs0.2198 94842 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.02 Å2
Refinement stepCycle: LAST / Resolution: 2.61→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23835 0 90 404 24329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224398
X-RAY DIFFRACTIONf_angle_d0.497233122
X-RAY DIFFRACTIONf_chiral_restr0.04033846
X-RAY DIFFRACTIONf_plane_restr0.00344238
X-RAY DIFFRACTIONf_dihedral_angle_d19.41088917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.670.40971340.32856191X-RAY DIFFRACTION92.91
2.67-2.750.32141420.30166650X-RAY DIFFRACTION99.82
2.75-2.830.34651440.29186662X-RAY DIFFRACTION99.82
2.83-2.920.34641410.27446630X-RAY DIFFRACTION99.79
2.92-3.020.30811420.26176647X-RAY DIFFRACTION99.69
3.02-3.140.2831420.256601X-RAY DIFFRACTION99.65
3.14-3.290.29981440.24296687X-RAY DIFFRACTION99.85
3.29-3.460.30091420.23086653X-RAY DIFFRACTION99.78
3.46-3.680.24311440.21116664X-RAY DIFFRACTION99.88
3.68-3.960.23551440.19746676X-RAY DIFFRACTION99.81
3.96-4.360.22411440.17656672X-RAY DIFFRACTION99.84
4.36-4.990.2051430.16616672X-RAY DIFFRACTION99.74
4.99-6.290.28161450.20086716X-RAY DIFFRACTION99.8
6.29-49.130.22391450.1816725X-RAY DIFFRACTION98.48
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)
10.302081475752-0.1957542842920.2404919837460.641471509809-0.1059162628840.4015382647030.0221461254545-0.0179389928193-0.00831721287895-0.115475336491-0.01110694161850.1367380779310.01408872780850.0058505909837-2.62932998824E-100.149938688988-0.0146310695684-0.03695114122050.1463967318770.0009039716664660.15833754396436.6271871226-18.96145119444.7630459659
20.125491220398-0.0112069083630.2125564317670.716331887784-0.07366422616940.60500983701-0.03959312084720.02206319182350.06593661478390.133089077966-0.00722474682942-0.115359029416-0.02262018723950.0042430988563-1.99521773062E-100.1343068693750.000470973434404-0.004936662224770.123740595573-0.01811789947890.1419433140028.06346671997-52.192994741513.7961677384
30.943014740632-0.196389482730.0345898903640.4380194120070.1282031177480.4181452514760.007205390813830.142684624902-0.0237109511158-0.03264786272280.06506620722210.04497864997680.00389720853595-0.0135856790293-5.48987518613E-110.121278672243-0.0154181136736-0.02261811428950.2564286246350.00906488681940.412360814546-21.2141591776-32.206085879249.3296838747
40.836294921375-0.2105534158310.4370375789170.6277603241310.1557658635460.503829834161-0.314616298997-0.04581392601310.05584569736390.339059878489-0.370938457025-0.890637441658-0.3402118350790.3849444306472.37559325275E-11-0.1908701487920.3690634834410.901319855771-0.275425298607-1.02220751257-2.44925491409-42.046700201-65.44562160759.4739483241
50.4277210547080.02864428027670.09568912851040.4973062047430.001276384753550.1702917117440.00881090828407-0.007529301462240.0276409765812-0.12295425686-0.01089825821410.2000713783090.00717174992407-0.005679458618245.29874430115E-110.169550710354-0.0101647249427-0.05358274662070.119447866025-0.0186138488960.15834471354634.4717078271-78.941383019446.2389674612
60.520690489401-0.1474511505460.05585741165690.466793707323-0.1175054149710.251210955560.00136226598120.01458153749830.0845293412685-0.0670105471211-0.02208092276230.0868097976261-0.003120211888130.0312033743624-2.16637522175E-100.123868780572-0.01976419806960.004666029471650.104960793403-0.01313468789430.129356052421-9.64834338778-48.8122412463-11.8237493409
70.9373440894750.189037313957-0.06912122032020.0834761829993-0.2487561159060.550843141514-0.0107301531804-0.292255053869-0.0136787521901-0.02656224408610.0100481964925-0.0843855965612-0.05301550039710.03759459814181.94612477098E-100.1392390693510.0184106392544-0.03539248626940.348617892965-0.04501326611770.4185753315433.61348382822-28.812626990267.7629238853
80.610301723007-0.01259251346080.01315163677440.5352705605270.02970649416090.09278633133650.04561778236040.0061033616067-0.0774250799029-0.088497435018-0.03180741171820.246443843534-0.00764452914650.038838779843-1.17609024143E-100.144607492604-0.01379364228970.02109981330110.135644748332-0.02232147860810.020396942717140.9928859697-62.3093477122-8.96661165466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 394)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 394)
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 394)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 394)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 394)
6X-RAY DIFFRACTION6(chain 'F' and resid 6 through 394)
7X-RAY DIFFRACTION7(chain 'G' and resid 6 through 394)
8X-RAY DIFFRACTION8(chain 'H' and resid 6 through 394)

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