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- PDB-8b35: Chalcone synthase from Hordeum vulgare complexed with CoA and nar... -

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Basic information

Entry
Database: PDB / ID: 8b35
TitleChalcone synthase from Hordeum vulgare complexed with CoA and naringenin
ComponentsChalcone synthase 2
KeywordsTRANSFERASE / POLYKETIDE SYNTHASE / CHALCONE BIOSYNTHESIS
Function / homology
Function and homology information


: / chalcone synthase / naringenin-chalcone synthase activity / flavonoid 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 / 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 15, 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)92,5536
Polymers90,4742
Non-polymers2,0804
Water6,612367
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-23 kcal/mol
Surface area26430 Å2
Unit cell
Length a, b, c (Å)73.908, 95.981, 138.338
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: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 12 - 391 / Label seq-ID: 30 - 409

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-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5 / 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.: 367 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
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, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→48.037 Å / Num. obs: 67109 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 19.8
Reflection shell

Num. unique obs: 67109 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
9.38-47.9911.30.0390.9990.0160.042
2-2.0513.50.4650.9790.190.503

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Processing

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

8b32


Resolution: 2→48.037 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.16 / SU B: 2.611 / SU ML: 0.074 / Average fsc free: 0.9535 / Average fsc work: 0.9621 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1934 3335 4.975 %
Rwork0.1589 63702 -
all0.161 --
obs-67037 99.869 %
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: 29.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.315 Å20 Å20 Å2
2--2.247 Å2-0 Å2
3----2.562 Å2
Refinement stepCycle: LAST / Resolution: 2→48.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 0 136 367 6307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155801
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.6388230
X-RAY DIFFRACTIONr_angle_other_deg1.4451.57613387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74422.174276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.995151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0181534
X-RAY DIFFRACTIONr_chiral_restr0.0860.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021279
X-RAY DIFFRACTIONr_nbd_refined0.2060.21105
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.25464
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22929
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2312
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.213
X-RAY DIFFRACTIONr_nbd_other0.1390.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.216
X-RAY DIFFRACTIONr_mcbond_it2.5462.7153050
X-RAY DIFFRACTIONr_mcbond_other2.5422.7143049
X-RAY DIFFRACTIONr_mcangle_it3.3264.0593809
X-RAY DIFFRACTIONr_mcangle_other3.3254.063810
X-RAY DIFFRACTIONr_scbond_it4.3133.3643012
X-RAY DIFFRACTIONr_scbond_other4.3133.3663013
X-RAY DIFFRACTIONr_scangle_it6.2714.8434421
X-RAY DIFFRACTIONr_scangle_other6.274.8454422
X-RAY DIFFRACTIONr_lrange_it7.17533.6676541
X-RAY DIFFRACTIONr_lrange_other7.15233.476475
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.0512013
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.081890.05008
12BX-RAY DIFFRACTIONLocal ncs0.081890.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2432510.1834621X-RAY DIFFRACTION99.918
2.052-2.1080.2122070.1654539X-RAY DIFFRACTION99.7688
2.108-2.170.192090.1564444X-RAY DIFFRACTION99.7855
2.17-2.2360.1712280.1464308X-RAY DIFFRACTION99.9119
2.236-2.310.1852310.1384151X-RAY DIFFRACTION99.9088
2.31-2.3910.1792070.1454003X-RAY DIFFRACTION99.7867
2.391-2.4810.1972130.1533909X-RAY DIFFRACTION100
2.481-2.5820.1651970.1483733X-RAY DIFFRACTION100
2.582-2.6970.2031830.1573629X-RAY DIFFRACTION100
2.697-2.8280.1871620.1593481X-RAY DIFFRACTION100
2.828-2.9810.2051630.1543297X-RAY DIFFRACTION99.9134
2.981-3.1620.1941740.1583101X-RAY DIFFRACTION99.939
3.162-3.380.211710.1642944X-RAY DIFFRACTION99.9358
3.38-3.6510.1941550.1632705X-RAY DIFFRACTION99.5129
3.651-3.9990.1881290.1632555X-RAY DIFFRACTION99.9628
3.999-4.4710.1781310.1422292X-RAY DIFFRACTION100
4.471-5.1620.1631170.1432045X-RAY DIFFRACTION100
5.162-6.3190.218910.191761X-RAY DIFFRACTION99.7308
6.319-8.9280.211690.1711373X-RAY DIFFRACTION99.2429

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