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- PDB-5wx5: Alkylquinolone synthase Y215V mutant from Evodia rutaecarpa -

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Basic information

Entry
Database: PDB / ID: 5wx5
TitleAlkylquinolone synthase Y215V mutant from Evodia rutaecarpa
ComponentsAlkylquinolone synthase
KeywordsTRANSFERASE / polyketide synthase
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
Alkylquinolone synthase
Similarity search - Component
Biological speciesTetradium ruticarpum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.058 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkylquinolone synthase
B: Alkylquinolone synthase
C: Alkylquinolone synthase
D: Alkylquinolone synthase
E: Alkylquinolone synthase
F: Alkylquinolone synthase


Theoretical massNumber of molelcules
Total (without water)272,7366
Polymers272,7366
Non-polymers00
Water00
1
A: Alkylquinolone synthase
B: Alkylquinolone synthase


Theoretical massNumber of molelcules
Total (without water)90,9122
Polymers90,9122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-20 kcal/mol
Surface area27040 Å2
MethodPISA
2
C: Alkylquinolone synthase
D: Alkylquinolone synthase


Theoretical massNumber of molelcules
Total (without water)90,9122
Polymers90,9122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-20 kcal/mol
Surface area27190 Å2
MethodPISA
3
E: Alkylquinolone synthase
F: Alkylquinolone synthase


Theoretical massNumber of molelcules
Total (without water)90,9122
Polymers90,9122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-21 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.160, 186.160, 139.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 4:239 or resseq 241:395))
21(chain B and (resseq 4:239 or resseq 241:395))
31(chain C and (resseq 4:239 or resseq 241:395))
41(chain D and (resseq 4:239 or resseq 241:395))
51(chain E and (resseq 4:239 or resseq 241:395))
61(chain F and (resseq 4:239 or resseq 241:395))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU(chain A and (resseq 4:239 or resseq 241:395))AA4 - 23916 - 251
12PROPROLEULEU(chain A and (resseq 4:239 or resseq 241:395))AA241 - 395253 - 407
21SERSERGLUGLU(chain B and (resseq 4:239 or resseq 241:395))BB4 - 23916 - 251
22PROPROLEULEU(chain B and (resseq 4:239 or resseq 241:395))BB241 - 395253 - 407
31SERSERGLUGLU(chain C and (resseq 4:239 or resseq 241:395))CC4 - 23916 - 251
32PROPROLEULEU(chain C and (resseq 4:239 or resseq 241:395))CC241 - 395253 - 407
41SERSERGLUGLU(chain D and (resseq 4:239 or resseq 241:395))DD4 - 23916 - 251
42PROPROLEULEU(chain D and (resseq 4:239 or resseq 241:395))DD241 - 395253 - 407
51SERSERGLUGLU(chain E and (resseq 4:239 or resseq 241:395))EE4 - 23916 - 251
52PROPROLEULEU(chain E and (resseq 4:239 or resseq 241:395))EE241 - 395253 - 407
61SERSERGLUGLU(chain F and (resseq 4:239 or resseq 241:395))FF4 - 23916 - 251
62PROPROLEULEU(chain F and (resseq 4:239 or resseq 241:395))FF241 - 395253 - 407

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Components

#1: Protein
Alkylquinolone synthase


Mass: 45455.977 Da / Num. of mol.: 6 / Mutation: Y215V
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: A0A1X8XLG0*PLUS
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 LC208544. Residues from MET (-11) to SER 0 are expression tags. This structure is Y215V 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M Sodium citrate, 1.99 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2015
RadiationMonochromator: Si(1111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.03
ReflectionResolution: 3.058→50 Å / Num. obs: 52842 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 14.9
Reflection shellResolution: 3.058→3.24 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.567
Highest resolutionLowest resolution
Rotation46.54 Å3.2 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WX4

5wx4


Resolution: 3.058→46.54 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 2643 5 %Random
Rwork0.1824 ---
obs0.1848 52842 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 188.9 Å2 / Biso mean: 53.3934 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: final / Resolution: 3.058→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18216 0 0 0 18216
Num. residues----2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818588
X-RAY DIFFRACTIONf_angle_d1.05225158
X-RAY DIFFRACTIONf_chiral_restr0.0562808
X-RAY DIFFRACTIONf_plane_restr0.0073282
X-RAY DIFFRACTIONf_dihedral_angle_d17.21111274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11464X-RAY DIFFRACTION4.553TORSIONAL
12B11464X-RAY DIFFRACTION4.553TORSIONAL
13C11464X-RAY DIFFRACTION4.553TORSIONAL
14D11464X-RAY DIFFRACTION4.553TORSIONAL
15E11464X-RAY DIFFRACTION4.553TORSIONAL
16F11464X-RAY DIFFRACTION4.553TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0582-3.11380.38961360.261825712707
3.1138-3.17370.31191380.244326272765
3.1737-3.23850.32441380.24126272765
3.2385-3.30890.29851380.220926202758
3.3089-3.38580.27971380.216426242762
3.3858-3.47050.24571380.201526182756
3.4705-3.56430.29161380.200526112749
3.5643-3.66910.26451370.189526202757
3.6691-3.78750.25781390.185926322771
3.7875-3.92280.22821360.178325942730
3.9228-4.07970.23061420.174326812823
4.0797-4.26530.19581370.163126162753
4.2653-4.490.1751400.153126532793
4.49-4.7710.18771390.148626382777
4.771-5.13890.18831390.152326452784
5.1389-5.65530.23311400.174726672807
5.6553-6.47160.24851410.189226652806
6.4716-8.14610.20421420.167927012843
8.1461-45.85920.21121470.172427882935

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