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- PDB-5yx4: Isoliquiritigenin-complexed Chalcone isomerase (S189A) from the A... -

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Basic information

Entry
Database: PDB / ID: 5yx4
TitleIsoliquiritigenin-complexed Chalcone isomerase (S189A) 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
Similarity search - Domain/homology
2',4,4'-TRIHYDROXYCHALCONE / Chalcone-flavonone isomerase family protein
Similarity search - Component
Biological speciesDeschampsia antarctica (Antarctic hairgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 14, 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

Downloads & links

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Assembly

Deposited unit
A: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3312
Polymers24,0741
Non-polymers2561
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint2 kcal/mol
Surface area11840 Å2
Unit cell
Length a, b, c (Å)83.221, 83.221, 93.127
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chalcone-flavonone isomerase family protein


Mass: 24074.264 Da / Num. of mol.: 1 / Mutation: S189A
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: Chemical ChemComp-HCC / 2',4,4'-TRIHYDROXYCHALCONE


Mass: 256.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.87 Å3/Da / Density % sol: 68.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.076 M sodium phosphate dibasic, 1.152 M potassium phosphate dibasic (pH 8.2)

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22153 / % possible obs: 99.5 % / Redundancy: 8.9 % / Net I/σ(I): 40.4
Reflection shellResolution: 2.1→2.14 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.1→41.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.335 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22602 1154 5.2 %RANDOM
Rwork0.18869 ---
obs0.19073 20971 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.014 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 19 218 1931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191750
X-RAY DIFFRACTIONr_bond_other_d0.0020.021636
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9712380
X-RAY DIFFRACTIONr_angle_other_deg1.09233789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14924.76263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97315263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.741155
X-RAY DIFFRACTIONr_chiral_restr0.1270.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211986
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02351
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9585.175927
X-RAY DIFFRACTIONr_mcbond_other4.9285.17926
X-RAY DIFFRACTIONr_mcangle_it6.0177.7241157
X-RAY DIFFRACTIONr_mcangle_other6.0177.731158
X-RAY DIFFRACTIONr_scbond_it6.0065.62823
X-RAY DIFFRACTIONr_scbond_other6.0025.619824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1638.2211224
X-RAY DIFFRACTIONr_long_range_B_refined9.99963.8172014
X-RAY DIFFRACTIONr_long_range_B_other9.96962.9071951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 55 -
Rwork0.241 1569 -
obs--98.78 %

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