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- PDB-1ee0: 2-PYRONE SYNTHASE COMPLEXED WITH ACETOACETYL-COA -

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Basic information

Entry
Database: PDB / ID: 1ee0
Title2-PYRONE SYNTHASE COMPLEXED WITH ACETOACETYL-COA
Components2-PYRONE SYNTHASE
KeywordsTRANSFERASE / polyketide synthase / thiolase fold
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
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
ACETOACETYL-COENZYME A / 2-pyrone synthase
Similarity search - Component
Biological speciesGerbera hybrid cultivar (plant)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsJez, J.M. / Austin, M.B. / Ferrer, J. / Bowmann, M.E. / Schroeder, J. / Noel, J.P.
CitationJournal: Chem.Biol. / Year: 2000
Title: Structural control of polyketide formation in plant-specific polyketide synthases.
Authors: Jez, J.M. / Austin, M.B. / Ferrer, J. / Bowman, M.E. / Schroder, J. / Noel, J.P.
History
DepositionJan 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-PYRONE SYNTHASE
B: 2-PYRONE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3704
Polymers87,6672
Non-polymers1,7032
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-2 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.406, 83.406, 240.625
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 2-PYRONE SYNTHASE


Mass: 43833.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gerbera hybrid cultivar (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P48391, chalcone synthase
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.5 M ammonium sulfate, 50 mM succinic acid (pH 5.5), 2 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
21.5 mMammonium sulfate1reservoir
350 mMsuccinic acid1reservoir
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.051→41.885 Å / Num. all: 61748 / Num. obs: 60757 / % possible obs: 98.2 % / Observed criterion σ(F): 0.01 / Observed criterion σ(I): 0 / Redundancy: 2.95 % / Biso Wilson estimate: 24.317 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.97 % / Rmerge(I) obs: 0.206 / Num. unique all: 3016 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 179623
Reflection shell
*PLUS
% possible obs: 98.1 % / Mean I/σ(I) obs: 4.5

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Processing

Software
NameClassification
EPMRphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.05→42 Å / σ(F): 0.01 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24307 3085 -random
Rwork0.18923 ---
all0.19383 61748 --
obs-60757 98.2 %-
Refinement stepCycle: LAST / Resolution: 2.05→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5802 0 108 541 6451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_deg2
X-RAY DIFFRACTIONp_bond_d0.014
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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