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- PDB-3a5r: Benzalacetone synthase from Rheum palmatum complexed with 4-couma... -

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Basic information

Entry
Database: PDB / ID: 3a5r
TitleBenzalacetone synthase from Rheum palmatum complexed with 4-coumaroyl-primed monoketide intermediate
ComponentsBenzalacetone synthase
KeywordsTRANSFERASE / benzalacetone synthase / chalcone synthase / type III polyketide synthase / Acyltransferase
Function / homology
Function and homology information


benzalacetone synthase / flavonoid biosynthetic process / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / protein homodimerization activity
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Polyketide synthase BAS
Similarity search - Component
Biological speciesRheum palmatum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMorita, H. / Kato, R. / Abe, I. / Sugio, S. / Kohno, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A structure-based mechanism for benzalacetone synthase from Rheum palmatum
Authors: Morita, H. / Shimokawa, Y. / Tanio, M. / Kato, R. / Noguchi, H. / Sugio, S. / Kohno, T. / Abe, I.
History
DepositionAug 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Benzalacetone synthase
B: Benzalacetone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3004
Polymers84,9722
Non-polymers3282
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-4 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.622, 89.847, 81.100
Angle α, β, γ (deg.)90.00, 100.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Benzalacetone synthase


Mass: 42485.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rheum palmatum (plant) / Gene: bas / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q94FV7
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 16% PEG8000, 0.1M sodium citrate, 0.15M potassium thiocyanate, Socking: 16% PEG8000, 0.1M sodium citrate, 0.15M potassium thiocyanate, 2mM 4-coumaroyl-CoA, pH5.6, VAPOR DIFFUSION, SITTING ...Details: 16% PEG8000, 0.1M sodium citrate, 0.15M potassium thiocyanate, Socking: 16% PEG8000, 0.1M sodium citrate, 0.15M potassium thiocyanate, 2mM 4-coumaroyl-CoA, pH5.6, VAPOR DIFFUSION, SITTING DROP, socking, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.82656 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 29, 2007
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 100874 / Num. obs: 100874 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.071 / Net I/σ(I): 32.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8.3 / Num. unique all: 10022 / Rsym value: 0.229 / % possible all: 99.3

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A5Q

3a5q


Resolution: 1.6→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 5108 -RANDOM
Rwork0.195 ---
all0.197 100844 --
obs0.197 100844 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 22 554 6372

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