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- PDB-7yj9: Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCH... -

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Basic information

Entry
Database: PDB / ID: 7yj9
TitleCrystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) complex with CoA and Naringenin
Componentschalcone synthase 1 (ScCHS1)
KeywordsTRANSFERASE / flavonoids biosynthesis / chalcone synthase / Stenoloma chusanum
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / COENZYME A / NARINGENIN
Function and homology information
Biological speciesOdontosoria chusana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsLi, J.X. / Cheng, A.X. / Zhang, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770330 China
National Natural Science Foundation of China (NSFC)32000228 China
National Natural Science Foundation of China (NSFC)31870720 China
CitationJournal: J Integr Plant Biol / Year: 2022
Title: Molecular and structural characterization of a promiscuous chalcone synthase from the fern species Stenoloma chusanum.
Authors: Ni, R. / Niu, M. / Fu, J. / Tan, H. / Zhu, T.T. / Zhang, J. / Lou, H.X. / Zhang, P. / Li, J.X. / Cheng, A.X.
History
DepositionJul 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Assembly

Deposited unit
A: chalcone synthase 1 (ScCHS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5463
Polymers44,5061
Non-polymers1,0402
Water5,603311
1
A: chalcone synthase 1 (ScCHS1)
hetero molecules

A: chalcone synthase 1 (ScCHS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0926
Polymers89,0122
Non-polymers2,0804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area9050 Å2
ΔGint-25 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.835, 72.395, 83.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

21A-654-

HOH

31A-717-

HOH

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Components

#1: Protein chalcone synthase 1 (ScCHS1)


Mass: 44506.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odontosoria chusana (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.851→36.197 Å / Num. obs: 31014 / % possible obs: 89.78 % / Redundancy: 12.1 % / CC1/2: 0.997 / Net I/σ(I): 19.3
Reflection shellResolution: 1.851→1.917 Å / Num. unique obs: 2018 / CC1/2: 0.687

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VEY

7vey


Resolution: 1.851→36.197 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 2000 6.45 %
Rwork0.153 29013 -
obs0.1555 31013 89.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.48 Å2 / Biso mean: 25.6579 Å2 / Biso min: 8.69 Å2
Refinement stepCycle: final / Resolution: 1.851→36.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 78 311 3361
Biso mean--42.07 33.36 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063112
X-RAY DIFFRACTIONf_angle_d0.9834236
X-RAY DIFFRACTIONf_chiral_restr0.06479
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d13.4781840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8512-1.89750.2635910.2205131358
1.8975-1.94880.20051030.175149365
1.9488-2.00610.21461120.1645163272
2.0061-2.07090.20791240.1665180079
2.0709-2.14490.20691360.1621197187
2.1449-2.23080.1961480.1565214294
2.2308-2.33230.19841580.15652295100
2.3323-2.45520.19721580.15872289100
2.4552-2.6090.21361570.16272287100
2.609-2.81040.23291580.16062302100
2.8104-3.0930.19681600.15672312100
3.093-3.54030.17931610.14372336100
3.5403-4.45910.14951630.12882363100
4.4591-36.1970.19461710.15362478100
Refinement TLS params.Method: refined / Origin x: -16.0415 Å / Origin y: -11.9315 Å / Origin z: 10.3401 Å
111213212223313233
T0.1145 Å2-0.0221 Å20.0296 Å2-0.1448 Å20.0267 Å2--0.14 Å2
L0.6993 °2-0.251 °20.1922 °2-1.422 °2-0.3367 °2--1.0246 °2
S0.0027 Å °-0.0418 Å °-0.1102 Å °0.1065 Å °0.0959 Å °0.2917 Å °0.1043 Å °-0.1832 Å °-0.0363 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 412
2X-RAY DIFFRACTION1allA420 - 421
3X-RAY DIFFRACTION1allS1 - 315

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