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- PDB-1eyp: CHALCONE ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 1eyp
TitleCHALCONE ISOMERASE
ComponentsCHALCONE-FLAVONONE ISOMERASE 1
KeywordsISOMERASE / chalcone isomerase
Function / homology
Function and homology information


chalcone isomerase / chalcone isomerase activity / flavonoid biosynthetic process
Similarity search - Function
Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / 10k-s Protein, Hypothetical Protein A; Chain A / Chalcone isomerase ...Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / 10k-s Protein, Hypothetical Protein A; Chain A / Chalcone isomerase / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chalcone--flavanone isomerase 1
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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 / 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 1
B: CHALCONE-FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)47,7022
Polymers47,7022
Non-polymers00
Water1,67593
1
A: CHALCONE-FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8511
Polymers23,8511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHALCONE-FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8511
Polymers23,8511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.370, 90.370, 352.860
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.36 Å3/Da / Density % sol: 71.77 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% glycerol 1.8 M ammonium sulfate 0.05 M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 302K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
225 %(v/v)glycerol1reservoir
31.8-2.0 Mammonium sulfate1reservoir
40.05 MPIPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.5→38.1 Å / Num. all: 30687 / Num. obs: 27821 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.4
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.407 / Num. unique all: 3726 / % possible all: 71.8
Reflection
*PLUS
Num. measured all: 86781
Reflection shell
*PLUS
% possible obs: 61.7 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→38.1 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1355 -random
Rwork0.249 ---
all-30687 --
obs-27821 90.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 0 93 3271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_angle_deg2
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 38.1 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.235 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg2

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