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- PDB-1i88: CHALCONE SYNTHASE (G256V) -

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Basic information

Entry
Database: PDB / ID: 1i88
TitleCHALCONE SYNTHASE (G256V)
ComponentsCHALCONE SYNTHASE 2
KeywordsTRANSFERASE / chalcone synthase / polyketide synthase
Function / homology
Function and homology information


chalcone biosynthetic process / chalcone synthase activity / chalcone synthase / naringenin-chalcone synthase activity / flavonoid 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: 1.45 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 ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8514
Polymers85,6592
Non-polymers1922
Water13,547752
1
A: CHALCONE SYNTHASE 2
hetero molecules

B: CHALCONE SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8514
Polymers85,6592
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
Buried area6500 Å2
ΔGint-36 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.292, 98.292, 129.676
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: 42829.355 Da / Num. of mol.: 2 / Mutation: G256V
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
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: BL9-2 / Wavelength: 1.01 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 1.45→46 Å / Num. all: 128835 / Num. obs: 1366179 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 29.7
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6150 / % possible all: 95.9
Reflection
*PLUS
Num. obs: 128367 / Num. measured all: 1366179
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.51

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→46 Å / σ(F): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 6412 -random
Rwork0.203 ---
all0.197 128367 --
obs-1366179 99.3 %-
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 1.45→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 10 752 6762
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.8
X-RAY DIFFRACTIONo_bond_d0.02
LS refinement shellResolution: 1.45→1.525 Å
RfactorNum. reflection% reflection
Rfree0.247 894 -
Rwork0.212 --
obs-16671 95.9 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.197
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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