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- PDB-1jx0: Chalcone Isomerase--Y106F mutant -

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Basic information

Entry
Database: PDB / ID: 1jx0
TitleChalcone Isomerase--Y106F mutant
ComponentsCHALCONE--FLAVONONE ISOMERASE 1
KeywordsISOMERASE / monomer / 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 / 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
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: 2.85 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3117
Polymers47,6702
Non-polymers6415
Water1,820101
1
A: CHALCONE--FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3805
Polymers23,8351
Non-polymers5444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHALCONE--FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9312
Polymers23,8351
Non-polymers961
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)96,62214
Polymers95,3414
Non-polymers1,28110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area7690 Å2
ΔGint-144 kcal/mol
Surface area34010 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-66 kcal/mol
Surface area18230 Å2
MethodPISA
5
A: CHALCONE--FLAVONONE ISOMERASE 1
hetero molecules

A: CHALCONE--FLAVONONE ISOMERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,75910
Polymers47,6702
Non-polymers1,0898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3590 Å2
ΔGint-88 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.56, 89.56, 351.66
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 23835.234 Da / Num. of mol.: 2 / Mutation: Y106F
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.: 4 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 4.27 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: glycerol, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %(v/v)glycerol1reservoir
22.0 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2001
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.8→58.16 Å / Num. all: 19709 / Num. obs: 19709 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 56.2 Å2 / Rsym value: 0.064 / Net I/σ(I): 19.9
Reflection shellResolution: 2.85→2.98 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2456 / Rsym value: 0.516 / % possible all: 88.3
Reflection
*PLUS
Highest resolution: 2.85 Å / Lowest resolution: 58 Å / Num. obs: 19000 / Num. measured all: 261225 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.516

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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 106

Resolution: 2.85→10 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 898 4.9 %random
Rwork0.274 ---
all-19992 --
obs-18476 92.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 0.311596 Å2 / ksol: 54.0715 e/Å3
Displacement parametersBiso mean: 68.85 Å2
Baniso -1Baniso -2Baniso -3
1-15.51 Å226.06 Å20 Å2
2--17.5 Å20 Å2
3----33.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.73 Å
Luzzati d res high-2.85
Refinement stepCycle: LAST / Resolution: 2.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 39 101 3333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ilq.parilq.top
X-RAY DIFFRACTION4sul.parsul.top
Refinement
*PLUS
Lowest resolution: 58 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.012

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