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- PDB-1i89: Chalcone synthase (G256L) -

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Basic information

Entry
Database: PDB / ID: 1i89
TitleChalcone synthase (G256L)
ComponentsCHALCONE SYNTHASE 2
KeywordsTRANSFERASE / chalcone synthase / polyketide synthase
Function / homology
Function and homology information


chalcone biosynthetic process / 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 / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-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 / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-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: 1.86 Å
AuthorsJez, J.M. / Bowman, M.E. / Noel, J.P.
CitationJournal: Biochemistry / Year: 2001
Title: Structure-guided programming of polyketide chain-length determination in chalcone synthase.
Authors: Jez, J.M. / Bowman, M.E. / Noel, J.P.
History
DepositionMar 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHALCONE SYNTHASE 2
B: CHALCONE SYNTHASE 2


Theoretical massNumber of molelcules
Total (without water)85,6872
Polymers85,6872
Non-polymers00
Water8,053447
1
A: CHALCONE SYNTHASE 2

B: CHALCONE SYNTHASE 2


Theoretical massNumber of molelcules
Total (without water)85,6872
Polymers85,6872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
Buried area6020 Å2
ΔGint-9 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.103, 98.103, 131.132
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CHALCONE SYNTHASE 2 / CHS2


Mass: 42843.383 Da / Num. of mol.: 2 / Mutation: G256L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30074, chalcone synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 42.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.2-2.4 M ammonium sulfate, 0.1 M PIPES, 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
22.2-2.4 Mammonium sulfate1reservoir
30.1 MPIPES1reservoirpH6.5
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.86→31.2 Å / Num. all: 62023 / Num. obs: 57245 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 19.174 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21.9
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 5.7 / % possible all: 85
Reflection
*PLUS
Num. measured all: 390574
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

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

Resolution: 1.86→31.2 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3050 -random
Rwork0.215 ---
obs-62023 97.3 %-
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 1.86→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 0 447 6433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.9
X-RAY DIFFRACTIONo_bond_d0.021
LS refinement shellResolution: 1.861→1.956 Å
RfactorNum. reflection% reflection
Rfree0.299 398 -
Rwork0.211 --
obs-7717 85 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg

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