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- PDB-7bur: Chalcone synthase from Glycine max (L.) Merr (soybean) complexed ... -

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Basic information

Entry
Database: PDB / ID: 7bur
TitleChalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin
ComponentsChalcone synthase 1
KeywordsTRANSFERASE / Isoflavonoid / Flavonoid / Soybean / PLANT PROTEIN
Function / homology
Function and homology information


chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / 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
CITRIC ACID / NARINGENIN / Chalcone synthase 1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsImaizumi, R. / Mameda, R. / Takeshita, K. / Waki, T. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. ...Imaizumi, R. / Mameda, R. / Takeshita, K. / Waki, T. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. / Yamashita, S. / Nakayama, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03938 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
CitationJournal: Proteins / Year: 2020
Title: Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean.
Authors: Imaizumi, R. / Mameda, R. / Takeshita, K. / Kubo, H. / Sakai, N. / Nakata, S. / Takahashi, S. / Kataoka, K. / Yamamoto, M. / Nakayama, T. / Yamashita, S. / Waki, T.
History
DepositionApr 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chalcone synthase 1
B: Chalcone synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6108
Polymers89,2972
Non-polymers1,3136
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-14 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.640, 97.990, 157.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chalcone synthase 1 / Naringenin-chalcone synthase 1


Mass: 44648.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: CHS1 / Plasmid: pCold I / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P24826, chalcone synthase
#2: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate (pH 5.6).

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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: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→47.73 Å / Num. obs: 1023907 / % possible obs: 100 % / Redundancy: 13.35 % / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rrim(I) all: 0.188 / Net I/σ(I): 15.76
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 12.72 % / Rmerge(I) obs: 1.868 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 12199 / CC1/2: 0.705 / Rrim(I) all: 1.946 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DXA

6dxa


Resolution: 1.82→47.73 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.826 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1926 3904 5.089 %
Rwork0.1506 --
all0.153 --
obs-76721 99.927 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.319 Å2
Baniso -1Baniso -2Baniso -3
1--1.821 Å2-0 Å2-0 Å2
2--0.561 Å2-0 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.82→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 92 731 6801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136377
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176021
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.6448678
X-RAY DIFFRACTIONr_angle_other_deg1.391.57314026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28322.893280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.881151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6441532
X-RAY DIFFRACTIONr_chiral_restr0.080.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027163
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021241
X-RAY DIFFRACTIONr_nbd_refined0.2070.21271
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.25614
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23077
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2575
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.210
X-RAY DIFFRACTIONr_nbd_other0.1910.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.232
X-RAY DIFFRACTIONr_mcbond_it1.9882.5173208
X-RAY DIFFRACTIONr_mcbond_other1.9752.5163207
X-RAY DIFFRACTIONr_mcangle_it2.6913.7644042
X-RAY DIFFRACTIONr_mcangle_other2.6963.7644043
X-RAY DIFFRACTIONr_scbond_it3.9643.1383169
X-RAY DIFFRACTIONr_scbond_other3.9543.1333166
X-RAY DIFFRACTIONr_scangle_it5.8614.5114635
X-RAY DIFFRACTIONr_scangle_other5.864.5134636
X-RAY DIFFRACTIONr_lrange_it7.78633.0387308
X-RAY DIFFRACTIONr_lrange_other7.70532.3517105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.82-1.8680.3432880.29852530.355680.7660.77899.51510.285
1.868-1.9190.2832540.24551960.24754500.8480.8561000.222
1.919-1.9740.2522750.20850430.2153180.8780.8921000.181
1.974-2.0350.2322890.1948870.19251760.9160.9241000.16
2.035-2.1020.2182740.17247300.17550040.9260.9371000.143
2.102-2.1750.1862540.15345960.15448500.9460.9541000.126
2.175-2.2570.1782440.14144430.14346870.9570.9621000.117
2.257-2.3490.2172150.13742960.14145110.9430.9651000.113
2.349-2.4530.1982110.13841360.14143470.9530.9641000.116
2.453-2.5730.1831940.13439460.13741400.9610.9691000.115
2.573-2.7110.2042080.13437530.13739610.9520.9691000.116
2.711-2.8750.21910.13935950.14237860.9550.9691000.121
2.875-3.0730.1951680.14833460.1535150.9560.96799.97150.133
3.073-3.3180.1891760.15631210.15832970.9620.9661000.145
3.318-3.6330.1861610.15629250.15730860.9690.9741000.149
3.633-4.0590.1661230.13126350.13327580.9750.9791000.129
4.059-4.6810.1341230.10923610.1124840.9810.9841000.113
4.681-5.7190.1541070.13320040.13421110.9820.9841000.136
5.719-8.0310.177890.15515990.15616880.9760.9771000.158
8.031-47.7350.234600.1589530.16110150.940.97399.8030.175

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