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- PDB-3awk: Crystal structure of the polyketide synthase 1 from huperzia serrata -

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Basic information

Entry
Database: PDB / ID: 3awk
TitleCrystal structure of the polyketide synthase 1 from huperzia serrata
ComponentsChalcone synthase-like polyketide synthase
KeywordsTRANSFERASE / type III polyketide synthase / chalcone synthase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / 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
Chalcone synthase-like polyketide synthase
Similarity search - Component
Biological speciesHuperzia serrata (toothed club-moss)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMorita, H. / Kondo, S. / Kato, R. / Sugio, S. / Kohno, T. / Abe, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Synthesis of unnatural alkaloid scaffolds by exploiting plant polyketide synthase.
Authors: Morita, H. / Yamashita, M. / Shi, S.P. / Wakimoto, T. / Kondo, S. / Kato, R. / Sugio, S. / Kohno, T. / Abe, I.
History
DepositionMar 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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: Chalcone synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9434
Polymers43,6631
Non-polymers2803
Water3,045169
1
A: Chalcone synthase-like polyketide synthase
hetero molecules

A: Chalcone synthase-like polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8868
Polymers87,3262
Non-polymers5616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area4740 Å2
ΔGint-5 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.3, 85.0, 137.7
Angle α, β, γ (deg.)90, 90, 90
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-458-

HOH

21A-519-

HOH

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Components

#1: Protein Chalcone synthase-like polyketide synthase / polyketide synthase 1


Mass: 43662.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Huperzia serrata (toothed club-moss) / Gene: Pks1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A3E7Z7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES-NaOH, 1925mM ammonium sulfate, 1,1,1,3,3,3-hexafluoro-2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, 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: Dec 15, 2006
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 27623 / Num. obs: 27623 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.056 / Net I/σ(I): 49.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 10.8 / Num. unique all: 2862 / Rsym value: 0.284 / % possible all: 100

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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: 1CGK

1cgk


Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 1427 RAMDOM
Rwork0.211 --
all0.214 27623 -
obs0.214 27623 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 17 169 3106
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.586
X-RAY DIFFRACTIONc_dihedral_angle_d23.63
X-RAY DIFFRACTIONc_improper_angle_d1.579

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