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- PDB-3ale: A type III polyketide synthase that produces diarylheptanoid -

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Basic information

Entry
Database: PDB / ID: 3ale
TitleA type III polyketide synthase that produces diarylheptanoid
ComponentsOs07g0271500 protein
KeywordsTRANSFERASE / type III polyketide synthase / benzalacetone synthase / diarylheptanoid
Function / homology
Function and homology information


bisdemethoxycurcumin synthase / bisdemethoxycurcumin synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / identical protein binding
Similarity search - Function
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
Bisdemethoxycurcumin synthase
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMorita, H. / Kato, R. / Sugio, S. / Abe, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for the one-pot formation of the diarylheptanoid scaffold by curcuminoid synthase from Oryza sativa
Authors: Morita, H. / Wanibuchi, K. / Nii, H. / Kato, R. / Sugio, S. / Abe, I.
History
DepositionAug 3, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Os07g0271500 protein
B: Os07g0271500 protein
C: Os07g0271500 protein
D: Os07g0271500 protein


Theoretical massNumber of molelcules
Total (without water)179,3804
Polymers179,3804
Non-polymers00
Water2,252125
1
A: Os07g0271500 protein
B: Os07g0271500 protein


Theoretical massNumber of molelcules
Total (without water)89,6902
Polymers89,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-8 kcal/mol
Surface area25410 Å2
MethodPISA
2
C: Os07g0271500 protein
D: Os07g0271500 protein


Theoretical massNumber of molelcules
Total (without water)89,6902
Polymers89,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-3 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.7, 97.2, 126.2
Angle α, β, γ (deg.)90, 103.7, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Os07g0271500 protein / curcuminoid synthase / Putative chalcone synthase


Mass: 44844.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Strain: japonica / Gene: OJ1001_C01.122, OSJNBb0002J01.6, Os07g0271500 / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8LIL0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE AT THE POSITION (RESIDUE 46) IS ILE ACCORDING TO DATABASE GENBANK AK109558.

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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: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1M HEPES-NaOH, 1.995M ammonium sulfate, 3% dimethylsulfoxide, 2mM coenzyme A, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5814 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 8, 2010
RadiationMonochromator: Cu K-alpha (anode) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5814 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 54813 / Num. obs: 54813 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.089 / Net I/σ(I): 21.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 5207 / Rsym value: 0.325 / % possible all: 88.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A5Q

3a5q


Resolution: 2.5→25.96 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2768 -RANDOM
Rwork0.221 ---
all0.226 54813 --
obs0.226 54813 92.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11098 0 0 125 11223

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