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- PDB-1fm7: CHALCONE ISOMERASE COMPLEXED WITH 5-DEOXYFLAVANONE -

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Basic information

Entry
Database: PDB / ID: 1fm7
TitleCHALCONE ISOMERASE COMPLEXED WITH 5-DEOXYFLAVANONE
ComponentsCHALCONE-FLAVONONE ISOMERASE 1
KeywordsISOMERASE / natural product biosynthesis / plant enzyme / chalcone / diffusion-limited
Function / homology
Function and homology information


chalcone isomerase / 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
7-HYDROXY-2-(4-HYDROXY-PHENYL)-CHROMAN-4-ONE / Chalcone--flavanone isomerase 1
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsJez, J.M. / Noel, J.P.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Reaction mechanism of chalcone isomerase. pH dependence, diffusion control, and product binding differences.
Authors: Jez, J.M. / Noel, J.P.
History
DepositionAug 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHALCONE-FLAVONONE ISOMERASE 1
B: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5037
Polymers47,7022
Non-polymers8015
Water3,405189
1
A: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3004
Polymers23,8511
Non-polymers4483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2043
Polymers23,8511
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-54 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.084, 90.084, 352.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CHALCONE-FLAVONONE ISOMERASE 1 / CHALCONE ISOMERASE 1


Mass: 23851.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: PET-28A(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P28012, chalcone isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DFV / 7-HYDROXY-2-(4-HYDROXY-PHENYL)-CHROMAN-4-ONE / 5-DEOXYFLAVANONE / Liquiritigenin


Mass: 256.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O4 / Comment: agonist*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 4.33 Å3/Da / Density % sol: 71.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8-2.0 M ammonium sulfate, 25% glycerol, 0.05 M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
225 %(v/v)glycerol1reservoir
35 %(v/v)ethanol1reservoir
42.0 Mammonium sulfate1reservoir
550 mMPIPES1reservoirpH6.5
62 mM4,2',4'-trihydroxychalcone1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0088
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 2.3→41 Å / Num. all: 428647 / Num. obs: 38491 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Redundancy: 11 % / Biso Wilson estimate: 53.5169 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 20.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.327 / Num. unique all: 1875 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 40.1 Å / Num. obs: 39067 / Num. measured all: 428647
Reflection shell
*PLUS
% possible obs: 98.6 % / Mean I/σ(I) obs: 3.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.3→41 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1853 -random
Rwork0.22 ---
all-428647 --
obs-38491 98.6 %-
Refinement stepCycle: LAST / Resolution: 2.3→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 53 189 3462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg2.1
X-RAY DIFFRACTIONo_bond_d0.019
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 41 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3

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