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- PDB-7cct: Quinolone synthase from Aegle marmelos Correa complexed with N-Me... -

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Basic information

Entry
Database: PDB / ID: 7cct
TitleQuinolone synthase from Aegle marmelos Correa complexed with N-Methylanthraniloyl-CoA
ComponentsType III polyketide synthase
KeywordsPLANT PROTEIN / Quinolone synthase / type III PKS
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
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-like
Similarity search - Domain/homology
: / N-Methylanthraniloyl-CoA / Type III polyketide synthase
Similarity search - Component
Biological speciesAegle marmelos (bael)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMallika, V. / Abhinav, K.V. / Frandsen, K.E.H. / Soniya, E.V.
Funding support India, Denmark, 2items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)09/716(0178)/2018-EMR-1 dated 26.04.2018 India
Novo Nordisk FoundationNNF21OC0071799 Denmark
CitationJournal: Commun Biol / Year: 2024
Title: Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity
Authors: Mallika, V. / Abhinav, K.V. / Frandsen, K.E.H. / Soniya, E.V.
History
DepositionJun 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 2.0Mar 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / audit_author / cell / chem_comp / chem_comp_atom / citation_author / entity / entity_src_gen / exptl_crystal_grow / pdbx_audit_support / pdbx_contact_author / pdbx_database_related / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.gene_src_common_name / _exptl_crystal_grow.pdbx_details / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.classification / _software.name / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Model completeness
Details: The structure was missing a Cadmium ion which is now modelled. Ligand orientation was slightly optimized.
Provider: author / Type: Coordinate replacement
Revision 2.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8993
Polymers42,8851
Non-polymers1,0132
Water68538
1
A: Type III polyketide synthase
hetero molecules

A: Type III polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7976
Polymers85,7712
Non-polymers2,0264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area5140 Å2
ΔGint-26 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.839, 148.839, 105.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Type III polyketide synthase / Quinolone synthase


Mass: 42885.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aegle marmelos (bael) / Production host: Escherichia coli (E. coli) / References: UniProt: M1HE54
#2: Chemical ChemComp-FWC / N-Methylanthraniloyl-CoA


Mass: 900.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43N8O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 0.1 HEPES (pH-7.5), 1.4 M sodium citrate tribasic dihydrate, 0.1M cadmium chloride hydrate After crystal obtained soaked 2mM N-Methylanthraniloyl-CoA dissolved in the same buffer for 30 minutes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→48.76 Å / Num. obs: 18090 / % possible obs: 96.23 % / Redundancy: 1.5 % / Biso Wilson estimate: 58.93 Å2 / Rrim(I) all: 0.336 / Net I/σ(I): 1.5
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 849 / Rrim(I) all: 0.0933

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wd7

3wd7


Resolution: 2.35→48.76 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.292 846 4.68 %
Rwork0.2309 --
obs0.2338 18064 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 59 38 2976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.1
X-RAY DIFFRACTIONf_dihedral_angle_d10.392413
X-RAY DIFFRACTIONf_chiral_restr0.058466
X-RAY DIFFRACTIONf_plane_restr0.007518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.50.39781380.34162938X-RAY DIFFRACTION99
2.5-2.690.40541460.32122875X-RAY DIFFRACTION98
2.69-2.960.42621460.34732823X-RAY DIFFRACTION95
2.96-3.390.41031360.3022735X-RAY DIFFRACTION92
3.39-4.270.28441390.22242815X-RAY DIFFRACTION94
4.27-48.760.20371410.16733032X-RAY DIFFRACTION99

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