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- PDB-1eyq: Chalcone isomerase and naringenin -

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Basic information

Entry
Database: PDB / ID: 1eyq
TitleChalcone isomerase and naringenin
ComponentsCHALCONE-FLAVONONE ISOMERASE 1
KeywordsISOMERASE / chalcone isomerase / flavonoid
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 / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / Chalcone isomerase - #10 / 10k-s Protein, Hypothetical Protein A; Chain A / Chalcone isomerase ...Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / Chalcone isomerase - #10 / 10k-s Protein, Hypothetical Protein A; Chain A / Chalcone isomerase / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NARINGENIN / Chalcone--flavanone isomerase 1
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsJez, J.M. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase.
Authors: Jez, J.M. / Bowman, M.E. / Dixon, R.A. / Noel, J.P.
History
DepositionMay 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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)48,7279
Polymers47,7022
Non-polymers1,0257
Water6,882382
1
A: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4125
Polymers23,8511
Non-polymers5604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3164
Polymers23,8511
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: CHALCONE-FLAVONONE ISOMERASE 1
B: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)97,45518
Polymers95,4054
Non-polymers2,05014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area9620 Å2
ΔGint-190 kcal/mol
Surface area32660 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-85 kcal/mol
Surface area17530 Å2
MethodPISA
5
A: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules

A: CHALCONE-FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,82310
Polymers47,7022
Non-polymers1,1218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3590 Å2
ΔGint-94 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.624, 88.624, 350.369
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: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: P28012, chalcone isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 4.16 Å3/Da / Density % sol: 70.44 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% glycerol, 1.8 M ammonium sulfate, 0.05 M PIPES, 5% ethanol, 2.5 mM naringenin, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 302K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
22.5 mM(2S/2R)-naringenin1reservoir
35 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→46.7 Å / Num. all: 697121 / Num. obs: 60531 / % possible obs: 85.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 28
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.65 / Num. unique all: 2085 / % possible all: 60.6
Reflection
*PLUS
Num. measured all: 697121
Reflection shell
*PLUS
% possible obs: 60.6 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.85→46.7 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2958 -random
Rwork0.237 ---
all-70732 --
obs-60531 85.6 %-
Refinement stepCycle: LAST / Resolution: 1.85→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 65 382 3667
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
Lowest resolution: 46.7 Å / σ(F): 2 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg2.1

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