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- PDB-6l5u: Quinolone synthase from Aegle marmelos Correa -

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Basic information

Entry
Database: PDB / ID: 6l5u
TitleQuinolone synthase from Aegle marmelos Correa
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
Type III polyketide synthase
Similarity search - Component
Biological speciesAegle marmelos (bael)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
DepositionOct 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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
Revision 2.0Mar 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_related / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness / Details: C164 modification (S-sulfinylation) / Provider: author / Type: Coordinate replacement
Revision 2.1May 8, 2024Group: Database references / Category: citation
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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)42,9171
Polymers42,9171
Non-polymers00
Water4,270237
1
A: Type III polyketide synthase

A: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)85,8352
Polymers85,8352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area4900 Å2
ΔGint-12 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.840, 149.840, 105.491
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21A-537-

HOH

31A-602-

HOH

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Components

#1: Protein Type III polyketide synthase


Mass: 42917.449 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 0.1M HEPES (pH-7.5), 1.4M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 3, 2016
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.85→81.86 Å / Num. all: 51180 / Num. obs: 38750 / % possible obs: 97.4 % / Redundancy: 11 % / Biso Wilson estimate: 36.09 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 1.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.133 / Num. unique obs: 1421 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.20.1_4487: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WD7

3wd7


Resolution: 1.85→31.83 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1922 5.01 %
Rwork0.1853 --
obs0.1871 38373 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→31.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 9 237 3118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.888
X-RAY DIFFRACTIONf_dihedral_angle_d6.607398
X-RAY DIFFRACTIONf_chiral_restr0.057459
X-RAY DIFFRACTIONf_plane_restr0.01507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.38051200.34432616X-RAY DIFFRACTION100
1.9-1.950.3271410.27752614X-RAY DIFFRACTION100
1.95-20.27371240.24382593X-RAY DIFFRACTION100
2-2.070.28991370.22262629X-RAY DIFFRACTION100
2.07-2.140.28881280.22452614X-RAY DIFFRACTION100
2.14-2.230.26191500.21952609X-RAY DIFFRACTION100
2.23-2.330.30261500.22282567X-RAY DIFFRACTION99
2.33-2.450.23871210.2182591X-RAY DIFFRACTION99
2.45-2.610.28811420.21932550X-RAY DIFFRACTION98
2.61-2.810.27571300.21922571X-RAY DIFFRACTION98
2.81-3.090.22891410.20522561X-RAY DIFFRACTION97
3.09-3.540.19371530.17482575X-RAY DIFFRACTION98
3.54-4.450.1861440.14092649X-RAY DIFFRACTION99
4.46-31.830.16571410.15072712X-RAY DIFFRACTION99

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