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- PDB-1u0v: An Aldol Switch Discovered in Stilbene Synthases Mediates Cycliza... -

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Basic information

Entry
Database: PDB / ID: 1u0v
TitleAn Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization of Specificity of Type III Polyketide Synthases: 18xCHS structure
ComponentsChalcone synthase 2
KeywordsTRANSFERASE / type III polyketide synthase / PKS / condensing enzyme / thiolase fold / alpha-beta-alpha-beta-alpha fold / aldol switch / catalytic triad / engineered resveratrol 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAustin, M.B. / Bowman, M.E. / Ferrer, J.-L. / Schroder, J. / Noel, J.P.
CitationJournal: Chem.Biol. / Year: 2004
Title: An Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases
Authors: Austin, M.B. / Bowman, M.E. / Ferrer, J.-L. / Schroder, J. / Noel, J.P.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: 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
B: Chalcone synthase 2


Theoretical massNumber of molelcules
Total (without water)85,7492
Polymers85,7492
Non-polymers00
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-12 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.638, 59.753, 82.539
Angle α, β, γ (deg.)90.00, 108.17, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A and B constitute the biological homodimer.

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Components

#1: Protein Chalcone synthase 2 / / Naringenin-chalcone synthase 2


Mass: 42874.324 Da / Num. of mol.: 2
Mutation: D96A, V98L, V99A, V100M, T131S, S133T, G134T, V135P, M137L, Y157V, M158G, M159V, Y160F, Q161H, L268K, K269G, D270A, G273D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Gene: CHS2 / Plasmid: pHIS8 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 716 / 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 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ammonium acetate, HEPES-Na+ buffer, ethylene glycol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 29, 2000
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→24.93 Å / Num. all: 52432 / Num. obs: 52432 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.8 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
ProDCdata collection
XDSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BI5

1bi5


Resolution: 1.9→24.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1532315.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2639 5 %RANDOM
Rwork0.192 ---
all0.193 52432 --
obs0.192 52432 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.0314 Å2 / ksol: 0.342929 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å21.4 Å2
2---2.71 Å20 Å2
3---4.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5881 0 0 716 6597
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.721.5
X-RAY DIFFRACTIONc_mcangle_it1.172
X-RAY DIFFRACTIONc_scbond_it12
X-RAY DIFFRACTIONc_scangle_it1.522.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 445 5.1 %
Rwork0.214 8245 -
obs-8690 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CISGLY_18X.PARAM

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