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- PDB-9kai: Crystal Structure of Chalcone Isomerase-like Protein from Physcom... -

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Basic information

Entry
Database: PDB / ID: 9kai
TitleCrystal Structure of Chalcone Isomerase-like Protein from Physcomitrella patens
ComponentsChalcone-flavonone isomerase family protein
KeywordsTRANSFERASE / Flavonoid / chalcone isomerase-like protein
Function / homologyChalcone--flavonone isomerase 3-like / intramolecular lyase activity / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / DI(HYDROXYETHYL)ETHER / Chalcone-flavonone isomerase family protein
Function and homology information
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsImaizumi, R. / Waki, T. / Yasuda, A. / Yanai, T. / Takeshita, K. / Sakai, N. / Yamamoto, M. / Nakayama, T. / Yamashita, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H05470 Japan
Japan Society for the Promotion of Science (JSPS)21H02115 Japan
Japan Society for the Promotion of Science (JSPS)24K23286 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101070 Japan
CitationJournal: To Be Published
Title: Structural basis, dynamics, and mode of action of enhancer of flavonoid production in metabolon
Authors: Imaizumi, R. / Waki, T. / Yasuda, A. / Yanai, T. / Takeshita, K. / Sakai, N. / Yamamoto, M. / Nakayama, T. / Yamashita, S.
History
DepositionOct 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,6566
Polymers25,3171
Non-polymers3395
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.540, 45.870, 76.350
Angle α, β, γ (deg.)90.000, 113.229, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chalcone-flavonone isomerase family protein


Mass: 25317.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_006757 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A9SRW1

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Non-polymers , 5 types, 141 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Magnesium chloride, PEG 6000 or PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 16352 / % possible obs: 99.8 % / Redundancy: 17 % / Biso Wilson estimate: 23.18 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.45 / Net I/σ(I): 10.8
Reflection shellResolution: 1.87→1.98 Å / Mean I/σ(I) obs: 1.15 / Num. unique obs: 2546 / CC1/2: 0.582 / Rrim(I) all: 6.02

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→35.53 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 816 4.99 %
Rwork0.1882 15526 -
obs0.1904 16342 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.28 Å2
Refinement stepCycle: LAST / Resolution: 1.87→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 21 136 1755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651685
X-RAY DIFFRACTIONf_angle_d0.82322290
X-RAY DIFFRACTIONf_chiral_restr0.0583260
X-RAY DIFFRACTIONf_plane_restr0.0057300
X-RAY DIFFRACTIONf_dihedral_angle_d17.5057626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.990.31071320.27812571X-RAY DIFFRACTION99.74
1.99-2.140.29361080.22642590X-RAY DIFFRACTION99.85
2.14-2.360.24371210.19472582X-RAY DIFFRACTION99.93
2.36-2.70.24891520.2052573X-RAY DIFFRACTION99.96
2.7-3.40.2411430.18732573X-RAY DIFFRACTION100
3.4-35.530.18971600.15582637X-RAY DIFFRACTION100

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