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- PDB-3wxz: The structure of the I375F mutant of CsyB -

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Basic information

Entry
Database: PDB / ID: 3wxz
TitleThe structure of the I375F mutant of CsyB
ComponentsPutative uncharacterized protein csyB
KeywordsTRANSFERASE / CsyB / Type III polyketide synthase / Acyltransferase
Function / homology
Function and homology information


type III polyketide synthase complex / tetraketide alpha-pyrone synthase activity / naringenin-chalcone synthase activity / polyketide biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
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
Acylalkylpyrone synthase csyB / Acylalkylpyrone synthase csyB
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsMori, T. / Yang, D. / Matsui, T. / Morita, H. / Fujii, I. / Abe, I.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural basis for the formation of acylalkylpyrones from two beta-ketoacyl units by the fungal type III polyketide synthase CsyB.
Authors: Mori, T. / Yang, D. / Matsui, T. / Hashimoto, M. / Morita, H. / Fujii, I. / Abe, I.
History
DepositionAug 13, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein csyB
B: Putative uncharacterized protein csyB


Theoretical massNumber of molelcules
Total (without water)90,6832
Polymers90,6832
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-5 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.900, 104.750, 73.160
Angle α, β, γ (deg.)90.00, 114.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein csyB / Type III polyketide synthase CsyB


Mass: 45341.344 Da / Num. of mol.: 2 / Mutation: I375F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: csyB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: Q53U84, UniProt: Q2U852*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM PIPES-NaOH, 6% PEG 4000, 250mM LiCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 17, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42426 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.268 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXY

3wxy


Resolution: 2.303→41.184 Å / σ(F): 1.36 / Phase error: 23.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 2198 5.18 %RANDAM
Rwork0.1733 ---
obs0.1755 42426 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→41.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5746 0 0 393 6139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075867
X-RAY DIFFRACTIONf_angle_d1.0387964
X-RAY DIFFRACTIONf_dihedral_angle_d12.9962126
X-RAY DIFFRACTIONf_chiral_restr0.066907
X-RAY DIFFRACTIONf_plane_restr0.0051035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3033-2.35690.25871400.219264994
2.3569-2.41580.2631410.2049268295
2.4158-2.48110.22531400.2076265395
2.4811-2.55410.26081410.2045268095
2.5541-2.63660.29631400.1976266095
2.6366-2.73080.25691430.1937271295
2.7308-2.84010.2491400.1918266395
2.8401-2.96930.25311410.1883268695
2.9693-3.12580.25181420.1853269095
3.1258-3.32150.20551410.1734269595
3.3215-3.57790.23251410.1698267295
3.5779-3.93760.20951420.152269995
3.9376-4.50680.17031420.1425269495
4.5068-5.67560.21241430.1524272395
5.6756-40.46010.17911450.1698274195

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