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- PDB-8b3c: Chalcone synthase from Hordeum vulgare complexed with CoA and eri... -

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Basic information

Entry
Database: PDB / ID: 8b3c
TitleChalcone synthase from Hordeum vulgare complexed with CoA and eriodictyol
ComponentsChalcone synthase 2
KeywordsTRANSFERASE / POLYKETIDE SYNTHASE / CHALCONE BIOSYNTHESIS
Function / homology
Function and homology information


chalcone synthase activity / 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 / Chem-ERD / Chalcone synthase 2
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, L. / Groves, M.R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)893122European Union
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Engineering a Plant Polyketide Synthase for the Biosynthesis of Methylated Flavonoids.
Authors: Peng, B. / Zhang, L. / He, S. / Oerlemans, R. / Quax, W.J. / Groves, M.R. / Haslinger, K.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 10, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chalcone synthase 2
B: Chalcone synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5856
Polymers90,4742
Non-polymers2,1124
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-31 kcal/mol
Surface area25960 Å2
Unit cell
Length a, b, c (Å)77.884, 97.817, 137.928
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 10 - 390 / Label seq-ID: 28 - 408

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Chalcone synthase 2 / Naringenin-chalcone synthase 2


Mass: 45236.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: CHS2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96562, chalcone synthase
#2: Chemical ChemComp-ERD / (2S)-2-(3,4-DIHYDROXYPHENYL)-5,7-DIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE


Mass: 288.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES/Imidazole pH6.5; 0.03M MgCl2 0.03M CaCl2; 16%Glycerol; 8% PEG4000

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→48.956 Å / Num. obs: 71897 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 17
Reflection shell

Num. unique obs: 71897 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
9.59-48.9111.10.0450.9980.0180.048
2-2.0412.50.9850.9470.4191.071

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B32

8b32


Resolution: 2→48.956 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.206 / SU B: 4.98 / SU ML: 0.129 / Average fsc free: 0.8713 / Average fsc work: 0.8835 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2337 3554 4.949 %
Rwork0.1984 68262 -
all0.2 --
obs-71816 99.949 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.623 Å2
Baniso -1Baniso -2Baniso -3
1-2.967 Å20 Å20 Å2
2--1.706 Å2-0 Å2
3----4.673 Å2
Refinement stepCycle: LAST / Resolution: 2→48.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5827 0 138 164 6129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155827
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6398260
X-RAY DIFFRACTIONr_angle_other_deg1.3231.57713442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94622280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.952151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0751536
X-RAY DIFFRACTIONr_chiral_restr0.0710.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021290
X-RAY DIFFRACTIONr_nbd_refined0.1980.21131
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.25417
X-RAY DIFFRACTIONr_nbtor_refined0.1590.22893
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2212
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.29
X-RAY DIFFRACTIONr_nbd_other0.2120.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.25
X-RAY DIFFRACTIONr_mcbond_it4.0914.7113058
X-RAY DIFFRACTIONr_mcbond_other4.0914.713057
X-RAY DIFFRACTIONr_mcangle_it4.9787.0623819
X-RAY DIFFRACTIONr_mcangle_other4.9787.0633820
X-RAY DIFFRACTIONr_scbond_it5.1275.4033028
X-RAY DIFFRACTIONr_scbond_other5.1265.4043029
X-RAY DIFFRACTIONr_scangle_it7.0687.9014441
X-RAY DIFFRACTIONr_scangle_other7.0677.9024442
X-RAY DIFFRACTIONr_lrange_it8.46856.7016457
X-RAY DIFFRACTIONr_lrange_other8.47556.6716442
X-RAY DIFFRACTIONr_ncsr_local_group_10.0780.0512037
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.078330.05008
12BX-RAY DIFFRACTIONLocal ncs0.078330.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3272520.334995X-RAY DIFFRACTION99.9429
2.052-2.1080.3322400.3034864X-RAY DIFFRACTION99.9413
2.108-2.1690.3242480.2854751X-RAY DIFFRACTION99.98
2.169-2.2360.2742290.2654585X-RAY DIFFRACTION99.9792
2.236-2.3090.282370.2444446X-RAY DIFFRACTION99.9787
2.309-2.390.3062220.244337X-RAY DIFFRACTION99.9561
2.39-2.4810.2751980.244176X-RAY DIFFRACTION99.9771
2.481-2.5820.2742190.2244015X-RAY DIFFRACTION99.9528
2.582-2.6970.2632100.2223872X-RAY DIFFRACTION99.9755
2.697-2.8280.2772010.2343679X-RAY DIFFRACTION99.9742
2.828-2.9810.2371860.213531X-RAY DIFFRACTION100
2.981-3.1620.2421650.23344X-RAY DIFFRACTION99.9715
3.162-3.380.2251750.2053162X-RAY DIFFRACTION99.97
3.38-3.6510.261360.1992936X-RAY DIFFRACTION99.9675
3.651-3.9990.2361500.1862691X-RAY DIFFRACTION99.9648
3.999-4.470.1711460.152472X-RAY DIFFRACTION99.9618
4.47-5.1610.1911250.1452185X-RAY DIFFRACTION100
5.161-6.3190.219880.1681883X-RAY DIFFRACTION99.9493
6.319-8.9270.154770.1481488X-RAY DIFFRACTION100

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