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- PDB-5yx3: Chalcone isomerase from the Antarctic vascular plant Deschampsia ... -

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Basic information

Entry
Database: PDB / ID: 5yx3
TitleChalcone isomerase from the Antarctic vascular plant Deschampsia Antarctica (DaCHI1)
ComponentsChalcone-flavonone isomerase family protein
KeywordsISOMERASE / Chalcone isomerase / Deschampsia antarctica
Function / homology
Function and homology information


chalcone isomerase activity / flavonoid biosynthetic process
Similarity search - Function
Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A ...Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chalcone-flavonone isomerase family protein
Similarity search - Component
Biological speciesDeschampsia antarctica (Antarctic hairgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLee, C.W. / Park, S. / Lee, J.H.
CitationJournal: PLoS ONE / Year: 2018
Title: Crystal structure and enzymatic properties of chalcone isomerase from the Antarctic vascular plant Deschampsia antarctica Desv.
Authors: Park, S.H. / Lee, C.W. / Cho, S.M. / Lee, H. / Park, H. / Lee, J. / Lee, J.H.
History
DepositionDec 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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-flavonone isomerase family protein
B: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)47,9182
Polymers47,9182
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-9 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.472, 113.635, 76.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chalcone-flavonone isomerase family protein / Chalcone isomerase


Mass: 23959.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deschampsia antarctica (Antarctic hairgrass)
Gene: CHI1 / Production host: Escherichia coli (E. coli) / References: UniProt: G4U3G8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2 M ammonium sulfate, 0.1 M MES (pH 7.3), 29% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 12542 / % possible obs: 98.3 % / Redundancy: 6.8 % / Net I/σ(I): 39.7
Reflection shellResolution: 2.7→2.75 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.7→32.27 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 608 4.87 %RANDOM
Rwork0.2218 ---
obs0.2244 12482 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→32.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 0 1 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063220
X-RAY DIFFRACTIONf_angle_d1.1414372
X-RAY DIFFRACTIONf_dihedral_angle_d16.3051118
X-RAY DIFFRACTIONf_chiral_restr0.044506
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.97160.37071480.30412905X-RAY DIFFRACTION97
2.9716-3.40120.35211480.26792944X-RAY DIFFRACTION98
3.4012-4.28360.28061430.21352992X-RAY DIFFRACTION99
4.2836-32.27240.23491690.19313033X-RAY DIFFRACTION97

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