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- PDB-8jrd: Chalcone synthase from Glycine max (L.) Merr (soybean) complexed ... -

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Basic information

Entry
Database: PDB / ID: 8jrd
TitleChalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A
Componentschalcone synthase
KeywordsTRANSFERASE / isoflavonoid / Flavonoid / Soybean
Function / homology
Function and homology information


: / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/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 / Thiolase-like
Similarity search - Domain/homology
COENZYME A / NARINGENIN / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / chalcone synthase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWaki, T. / Imaizumi, R. / Nakata, S. / Yanai, T. / Takeshita, K. / Sakai, N. / Kataoka, K. / Yamamoto, M. / Nakayama, T. / Yamashita, S.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H05470 Japan
Japan Society for the Promotion of Science (JSPS)21H02115 Japan
Japan Society for the Promotion of Science (JSPS)22KJ1466 Japan
Japan Society for the Promotion of Science (JSPS)22K14823 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural insights into catalytic promiscuity of chalcone synthase from Glycine max (L.) Merr.: Coenzyme A-induced alteration of product specificity.
Authors: Waki, T. / Imaizumi, R. / Uno, K. / Doi, Y. / Tsunashima, M. / Yamada, S. / Mameda, R. / Nakata, S. / Yanai, T. / Takeshita, K. / Sakai, N. / Kataoka, K. / Yamamoto, M. / Takahashi, S. / ...Authors: Waki, T. / Imaizumi, R. / Uno, K. / Doi, Y. / Tsunashima, M. / Yamada, S. / Mameda, R. / Nakata, S. / Yanai, T. / Takeshita, K. / Sakai, N. / Kataoka, K. / Yamamoto, M. / Takahashi, S. / Nakayama, T. / Yamashita, S.
History
DepositionJun 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chalcone synthase
B: chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,46620
Polymers89,2972
Non-polymers3,16918
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint1 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.610, 97.470, 157.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein chalcone synthase


Mass: 44648.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: ICHS1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6X0M8

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Non-polymers , 6 types, 721 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.2 M ammonium acetate, 0.1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 75109 / % possible obs: 100 % / Redundancy: 15.66 % / CC1/2: 0.997 / Rrim(I) all: 0.22 / Net I/σ(I): 12.94
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 2.29 / Num. unique obs: 11886 / CC1/2: 0.745 / Rrim(I) all: 1.33 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→48.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.544 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18514 3744 5 %RANDOM
Rwork0.1502 ---
obs0.15194 71283 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0 Å2
2--0.28 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.83→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 207 703 6898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136357
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176044
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6528602
X-RAY DIFFRACTIONr_angle_other_deg1.4171.57314060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72722.727275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.969151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6651530
X-RAY DIFFRACTIONr_chiral_restr0.0860.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026936
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.711.983135
X-RAY DIFFRACTIONr_mcbond_other1.6941.9793134
X-RAY DIFFRACTIONr_mcangle_it2.3272.9623924
X-RAY DIFFRACTIONr_mcangle_other2.3322.9623925
X-RAY DIFFRACTIONr_scbond_it3.6362.6063222
X-RAY DIFFRACTIONr_scbond_other3.6362.6083223
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4193.6934679
X-RAY DIFFRACTIONr_long_range_B_refined6.97426.8517236
X-RAY DIFFRACTIONr_long_range_B_other6.83826.1787039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 252 -
Rwork0.254 5229 -
obs--99.96 %

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