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- PDB-1jwx: Chalcone Synthase--F215S mutant -

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Basic information

Entry
Database: PDB / ID: 1jwx
TitleChalcone Synthase--F215S mutant
ComponentsCHALCONE SYNTHASE 2
KeywordsTRANSFERASE / polyketide synthase / altered substrate specificity / ketoacyl synthase
Function / homology
Function and homology information


chalcone biosynthetic process / chalcone synthase activity / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.63 Å
AuthorsJez, J.M. / Bowman, M.E. / Noel, J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Expanding the biosynthetic repertoire of plant type III polyketide synthases by altering starter molecule specificity.
Authors: Jez, J.M. / Bowman, M.E. / 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: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHALCONE SYNTHASE 2


Theoretical massNumber of molelcules
Total (without water)42,7271
Polymers42,7271
Non-polymers00
Water6,197344
1
A: CHALCONE SYNTHASE 2

A: CHALCONE SYNTHASE 2


Theoretical massNumber of molelcules
Total (without water)85,4542
Polymers85,4542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area5990 Å2
ΔGint-11 kcal/mol
Surface area27390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.805, 97.805, 65.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-396-

HOH

21A-406-

HOH

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Components

#1: Protein CHALCONE SYNTHASE 2 / / NARINGENIN-CHALCONE SYNTHASE 2


Mass: 42727.184 Da / Num. of mol.: 1 / Mutation: F215S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Gene: CHS2 / Plasmid: pHIS8 (modified pET28b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P30074, chalcone synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, PIPES, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / Details: Ferrer, J.L., (1999) Nature Struct. Biol., 6, 775.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
22.2-2.4 Mammonium sulfate1reservoir
30.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 11, 1999
RadiationMonochromator: Pt coated / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.63→26 Å / Num. all: 43804 / Num. obs: 43804 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 3.5 / Net I/σ(I): 27.5
Reflection shellResolution: 1.62→1.67 Å / Redundancy: 3 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 2454 / Rsym value: 12.1 / % possible all: 81.6
Reflection
*PLUS
Lowest resolution: 26 Å / Num. measured all: 226775 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 81.6 % / Rmerge(I) obs: 0.12

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: wild-type CHS with Phe215 mutated to alanine

Resolution: 1.63→26 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2197 5 %random
Rwork0.19 ---
all0.2 43804 --
obs0.2 43804 95.9 %-
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.63→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 0 344 3328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d2.1
Refinement
*PLUS
Lowest resolution: 26 Å / % reflection Rfree: 5 % / Rfactor all: 0.2 / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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