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- PDB-1u0u: An Aldol Switch Discovered in Stilbene Synthases Mediates Cycliza... -

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Basic information

Entry
Database: PDB / ID: 1u0u
TitleAn Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases: Pine stilbene synthase structure
ComponentsDihydropinosylvin synthase
KeywordsTRANSFERASE / PKS / type III polyketide synthase / condensing enzyme / thiolase fold / alpha-beta-alpha-beta-alpha fold / aldol switch / catalytic triad
Function / homology
Function and homology information


pinosylvin synthase / pinosylvin synthase activity / biosynthetic process / cytoplasm
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 speciesPinus sylvestris (Scots pine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropinosylvin synthase
B: Dihydropinosylvin synthase
C: Dihydropinosylvin synthase
D: Dihydropinosylvin synthase
E: Dihydropinosylvin synthase
F: Dihydropinosylvin synthase


Theoretical massNumber of molelcules
Total (without water)258,7346
Polymers258,7346
Non-polymers00
Water33,7061871
1
A: Dihydropinosylvin synthase
B: Dihydropinosylvin synthase


Theoretical massNumber of molelcules
Total (without water)86,2452
Polymers86,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-14 kcal/mol
Surface area27020 Å2
MethodPISA
2
C: Dihydropinosylvin synthase
D: Dihydropinosylvin synthase


Theoretical massNumber of molelcules
Total (without water)86,2452
Polymers86,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-11 kcal/mol
Surface area26880 Å2
MethodPISA
3
E: Dihydropinosylvin synthase
F: Dihydropinosylvin synthase


Theoretical massNumber of molelcules
Total (without water)86,2452
Polymers86,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-15 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.221, 361.291, 57.317
Angle α, β, γ (deg.)90.00, 98.39, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe six STS monomers in the asymmetric unit comprise three biological homodimers: these independent dyads are formed by chains AB, CD, and EF.

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Components

#1: Protein
Dihydropinosylvin synthase / Stilbene synthase / STS / Pinosylvin-forming stilbene synthase


Mass: 43122.312 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pinus sylvestris (Scots pine) / Gene: PSS1 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q02323, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1871 / 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: 2.28 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, ammonium acetate, MOPSO-Na+, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2000
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.11→54.1 Å / Num. all: 103325 / Num. obs: 103258 / % possible obs: 78.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2
Reflection shellResolution: 2.1→2.23 Å / % possible all: 38.1

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Processing

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

1bi5


Resolution: 2.11→54.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3152607.22 / 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
Rfree0.289 5163 5 %RANDOM
Rwork0.225 ---
all0.228 103258 --
obs0.225 103258 78.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.9992 Å2 / ksol: 0.360649 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å2-2.34 Å2
2---2.63 Å20 Å2
3----1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.11→54.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17874 0 0 1871 19745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.982
X-RAY DIFFRACTIONc_scangle_it3.952.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 425 5 %
Rwork0.303 8018 -
obs-8443 38.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CISGLY_STS.PARAM

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