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

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Basic information

Entry
Database: PDB / ID: 7yjb
TitleCrystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) complex with CoA and Eriodictyol
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 / Chem-ERD
Function and homology information
Biological speciesOdontosoria chusana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)45,5623
Polymers44,5061
Non-polymers1,0562
Water5,639313
1
A: chalcone synthase 1 (ScCHS1)
hetero molecules

A: chalcone synthase 1 (ScCHS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1246
Polymers89,0122
Non-polymers2,1124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area9250 Å2
ΔGint-32 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.241, 72.507, 83.214
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-626-

HOH

21A-725-

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-ERD / (2S)-2-(3,4-DIHYDROXYPHENYL)-5,7-DIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE


Mass: 288.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O6 / 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.: 313 / 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: 2.25 Å3/Da / Density % sol: 45.21 %
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 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→41.61 Å / Num. obs: 24993 / % possible obs: 90.06 % / Redundancy: 12.4 % / CC1/2: 0.988 / Net I/σ(I): 16.6
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 1709 / CC1/2: 0.797

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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: 2→41.607 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 2000 8 %
Rwork0.1752 22987 -
obs0.1779 24987 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.74 Å2 / Biso mean: 29.0756 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 2→41.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 70 313 3355
Biso mean--54.66 33.76 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153113
X-RAY DIFFRACTIONf_angle_d1.584238
X-RAY DIFFRACTIONf_chiral_restr0.407479
X-RAY DIFFRACTIONf_plane_restr0.007533
X-RAY DIFFRACTIONf_dihedral_angle_d17.611131
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0004-2.05040.2395950.2039110161
2.0504-2.10580.24871040.192118167
2.1058-2.16780.25561150.1871131973
2.1678-2.23780.23161220.1912141478
2.2378-2.31770.24121340.1801152785
2.3177-2.41050.22211480.1862171295
2.4105-2.52020.22181570.1969180599
2.5202-2.65310.24941580.19531809100
2.6531-2.81930.24861560.19351805100
2.8193-3.03690.21981590.19011820100
3.0369-3.34240.22631600.18251833100
3.3424-3.82570.19121590.15611839100
3.8257-4.81890.15371620.14471863100
4.8189-41.6070.20281710.17311959100

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