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- PDB-1jx1: Chalcone Isomerase--T48A mutant -

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Basic information

Entry
Database: PDB / ID: 1jx1
TitleChalcone Isomerase--T48A mutant
ComponentsCHALCONE--FLAVONONE ISOMERASE 1
KeywordsISOMERASE / open-faced beta sandwich / unique fold
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 / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase superfamily / 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 / 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / Chalcone isomerase superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJez, J.M. / Bowman, M.E. / Noel, J.P.
Citation
Journal: Biochemistry / Year: 2002
Title: Role of Hydrogen Bonds in the Reaction Mechanism of Chalcone Isomerase
Authors: Jez, J.M. / Bowman, M.E. / Noel, J.P.
#1: Journal: 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
DepositionSep 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: CHALCONE--FLAVONONE ISOMERASE 1
D: CHALCONE--FLAVONONE ISOMERASE 1
E: CHALCONE--FLAVONONE ISOMERASE 1
F: CHALCONE--FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,47210
Polymers142,9276
Non-polymers5444
Water9,332518
1
A: CHALCONE--FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHALCONE--FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9172
Polymers23,8211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CHALCONE--FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2704
Polymers23,8211
Non-polymers4483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CHALCONE--FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CHALCONE--FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: CHALCONE--FLAVONONE ISOMERASE 1


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.94, 90.94, 349.99
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 23821.209 Da / Num. of mol.: 6 / Mutation: T48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: pHIS8 (modified pET28b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28012, chalcone isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 256.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O4 / Comment: agonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: glycerol, ammonium sulfate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %(v/v)glycerol1reservoir
22.2 Mammonium sulfate1reservoir
30.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 2001
RadiationMonochromator: flat mirror, single crystal, bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→78.76 Å / Num. all: 63669 / Num. obs: 63669 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.068 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 9063 / Rsym value: 0.486 / % possible all: 70.3
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 79.1 Å / Num. measured all: 326009 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 70.3 % / Rmerge(I) obs: 0.486

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wild-type chalcone isomerase with alanine at position 48

Resolution: 2.3→78.76 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3080 4.8 %random
Rwork0.23 ---
all-63669 --
obs-63669 88.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 58.8135 Å2 / ksol: 0.358359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.74 Å212.18 Å20 Å2
2--4.74 Å20 Å2
3----9.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→78.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9703 0 34 518 10255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dfl.pardfl.top
X-RAY DIFFRACTION4sul.parsul.top
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 79.1 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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