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- PDB-5wx7: Alkyldiketide-CoA synthase W332G mutant from Evodia rutaecarpa -

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Basic information

Entry
Database: PDB / ID: 5wx7
TitleAlkyldiketide-CoA synthase W332G mutant from Evodia rutaecarpa
ComponentsAlkyldiketide-CoA synthase
KeywordsTRANSFERASE / polyketidesynthase
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
COENZYME A / Alkyldiketide-CoA synthase
Similarity search - Component
Biological speciesTetradium ruticarpum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.904 Å
AuthorsMatsui, T. / Kodama, T. / Tadakoshi, T. / Morita, H.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: 2-Alkylquinolone alkaloid biosynthesis in the medicinal plant Evodia rutaecarpa involves collaboration of two novel type III polyketide synthases
Authors: Matsui, T. / Kodama, T. / Mori, T. / Tadakoshi, T. / Noguchi, H. / Abe, I. / Morita, H.
History
DepositionJan 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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: Alkyldiketide-CoA synthase
B: Alkyldiketide-CoA synthase
C: Alkyldiketide-CoA synthase
D: Alkyldiketide-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,56512
Polymers176,1114
Non-polymers3,4548
Water15,241846
1
A: Alkyldiketide-CoA synthase
B: Alkyldiketide-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7836
Polymers88,0552
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-36 kcal/mol
Surface area25330 Å2
MethodPISA
2
C: Alkyldiketide-CoA synthase
D: Alkyldiketide-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7836
Polymers88,0552
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-35 kcal/mol
Surface area25690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.760, 83.870, 136.140
Angle α, β, γ (deg.)90.000, 124.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Alkyldiketide-CoA synthase


Mass: 44027.695 Da / Num. of mol.: 4 / Mutation: W332G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetradium ruticarpum (plant) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A1X8XLG2*PLUS
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 846 / 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 deposited to GenBank as LC208543. Residues from MET (-11) to SER 0 are expression tags. This structure is W332G mutant.

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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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1 M MES, 0.2 M lithium sulfate, 25%(w/v) PEG3350, 10 mM CoASH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.03
ReflectionResolution: 1.9→47.248 Å / Num. obs: 118399 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.409 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.081 / Χ2: 1.009 / Net I/σ(I): 11.81 / Num. measured all: 403637
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.9-2.023.2880.5192.360.819198.4
2.02-2.163.4290.3313.810.902199.6
2.16-2.333.4830.2085.980.956199.6
2.33-2.553.3220.1378.240.977199.6
2.55-2.853.540.09312.090.99199.7
2.85-3.293.3610.0617.550.995199.5
3.29-4.033.5460.04226.20.997199.4
4.03-5.683.3520.03530.750.997199
5.68-47.2483.3690.03232.60.998198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.33 Å47.25 Å
Translation7.33 Å47.25 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.6.0phasing
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WX3

5wx3


Resolution: 1.904→47.248 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.89
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 6104 5.16 %RANDOM
Rwork0.198 ---
obs0.1999 118397 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.96 Å2 / Biso mean: 31.5046 Å2 / Biso min: 18.07 Å2
Refinement stepCycle: final / Resolution: 1.904→47.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11516 0 212 846 12574
Biso mean--48.56 33.45 -
Num. residues----1482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811970
X-RAY DIFFRACTIONf_angle_d0.94616227
X-RAY DIFFRACTIONf_chiral_restr0.0531800
X-RAY DIFFRACTIONf_plane_restr0.0062063
X-RAY DIFFRACTIONf_dihedral_angle_d18.1454411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9044-1.93720.37352860.34215431571792
1.9372-1.97240.30982950.31155605590095
1.9724-2.01040.31962950.29235590588595
2.0104-2.05140.32672960.27895625592195
2.0514-2.0960.29262950.275613590895
2.096-2.14480.29522960.25825629592595
2.1448-2.19840.28492930.2455559585295
2.1984-2.25780.24562970.24495643594095
2.2578-2.32430.29742950.2425608590395
2.3243-2.39930.2522970.23265634593195
2.3993-2.4850.26962950.22585621591695
2.485-2.58450.26532960.22725618591495
2.5845-2.70210.24622970.225642593995
2.7021-2.84460.24922960.2135619591595
2.8446-3.02280.26442960.20455632592895
3.0228-3.25610.21312970.18655645594295
3.2561-3.58370.21612970.17035645594295
3.5837-4.10190.20142990.14955667596695
4.1019-5.16680.17522980.13825676597494
5.1668-45.38850.20553040.17215759606394

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