[English] 日本語
Yorodumi
- PDB-7cct: Quinolone synthase from Aegle marmelos Correa complexed with N-Me... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more