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- PDB-3wd8: TypeIII polyketide synthases -

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Basic information

Entry
Database: PDB / ID: 3wd8
TitleTypeIII polyketide synthases
ComponentsType III polyketide synthase quinolone synthase
KeywordsTRANSFERASE / quinolone synthase / Type III polyketide synthase / Acyltransferase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
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
Type III polyketide synthase quinolone synthase
Similarity search - Component
Biological speciesCitrus microcarpa (calamondin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.463 Å
AuthorsMori, T. / Shimokawa, Y. / Matsui, T. / Morita, H. / Abe, I.
CitationJournal: To be Published
Title: Cloning, characterization, and crystal structure analysis of novel type III polyketide synthases from Citrus microcarpa
Authors: Mori, T. / Shimokawa, Y. / Matsui, T. / Kinjo, K. / Kato, R. / Noguchi, H. / Sugio, S. / Morita, H. / Abe, I.
History
DepositionJun 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Type III polyketide synthase quinolone synthase
B: Type III polyketide synthase quinolone synthase
C: Type III polyketide synthase quinolone synthase
D: Type III polyketide synthase quinolone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,1416
Polymers177,9574
Non-polymers1842
Water3,567198
1
A: Type III polyketide synthase quinolone synthase
B: Type III polyketide synthase quinolone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0713
Polymers88,9782
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-30 kcal/mol
Surface area26690 Å2
MethodPISA
2
C: Type III polyketide synthase quinolone synthase
D: Type III polyketide synthase quinolone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0713
Polymers88,9782
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-32 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.724, 135.912, 107.623
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Type III polyketide synthase quinolone synthase


Mass: 44489.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus microcarpa (calamondin) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: U3KRF1*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN THE UNIPROT DATABASE. ...THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN THE UNIPROT DATABASE. THIS SEQUENCE HAS ALREADY BEEN DAPOSITED TO GENBANK AS AB823730. RESIDUES FROM MET (-11) TO SER 0 ARE EXPRESSION TAGS.

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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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50mM Tris-HCl, 18% PEG3350, 4%(v/v) 1-propanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.463→19.987 Å / Num. all: 52974 / Num. obs: 52852 / % possible obs: 99.4 % / Biso Wilson estimate: 43.44 Å2
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 3.85 % / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CGK

1cgk


Resolution: 2.463→19.987 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7927 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 2689 5.09 %RANDOM
Rwork0.1945 ---
obs0.1969 52852 98.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.42 Å2 / Biso mean: 39.0751 Å2 / Biso min: 13.51 Å2
Refinement stepCycle: LAST / Resolution: 2.463→19.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12028 0 12 198 12238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112282
X-RAY DIFFRACTIONf_angle_d1.30116598
X-RAY DIFFRACTIONf_chiral_restr0.081868
X-RAY DIFFRACTIONf_plane_restr0.0082140
X-RAY DIFFRACTIONf_dihedral_angle_d14.3794580
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4635-2.50820.39691190.31582404252390
2.5082-2.55630.40131370.29962629276698
2.5563-2.60840.34671240.2842631275598
2.6084-2.6650.3131320.26722619275198
2.665-2.72690.3471390.2612640277998
2.7269-2.79490.29311650.25682598276399
2.7949-2.87020.32231500.24692649279998
2.8702-2.95440.33761570.24542595275299
2.9544-3.04950.3311450.23772649279498
3.0495-3.15810.27961480.2242622277099
3.1581-3.2840.27351210.21632660278199
3.284-3.43270.25391480.194726832831100
3.4327-3.61270.25551510.188226592810100
3.6127-3.83750.18451370.177226582795100
3.8375-4.13140.19071310.16127042835100
4.1314-4.54280.20761470.151726722819100
4.5428-5.19010.17581420.143427352877100
5.1901-6.50130.21361470.18226802827100
6.5013-19.98730.1781490.16812676282599

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