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- PDB-6ra3: Structural basis for recognition and ring-cleavage of the Pseudom... -

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Basic information

Entry
Database: PDB / ID: 6ra3
TitleStructural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC in complex with its product
ComponentsPutative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
KeywordsHYDROLASE / dioxygenase / alpha/beta hydrolase fold / catalytic triad / quorum sensing / Pseudomonas quinolone signal / Pseudomonas aeruginosa
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
Uteroglobin - #20 / Uteroglobin / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-(octanoylamino)benzoic acid / Dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
Similarity search - Component
Biological speciesMycobacteroides abscessus subsp. abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWullich, S. / Kobus, S. / Smits, S.H. / Fetzner, S.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqdC, a mycobacterial dioxygenase of the alpha / beta-hydrolase fold family.
Authors: Wullich, S.C. / Kobus, S. / Wienhold, M. / Hennecke, U. / Smits, S.H.J. / Fetzner, S.
History
DepositionApr 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 29, 2020Group: Refinement description / Category: refine_ls_shell / Item: _refine_ls_shell.d_res_low
Revision 2.0Jun 24, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 24, 2024Group: 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: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
F: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
E: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6564
Polymers89,3933
Non-polymers2631
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint6 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.173, 96.173, 189.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-371-

HOH

21F-494-

HOH

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Components

#1: Protein Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)


Mass: 29797.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus subsp. abscessus (bacteria)
Gene: SAMEA2070698_02780, SAMEA2161603_04096, SAMEA2275805_05965
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M8M580
#2: Chemical ChemComp-JWH / 2-(octanoylamino)benzoic acid


Mass: 263.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.10 to 0.15 M magnesium chloride, 0.1 M sodium chloride, 0.1 M MES pH 6.5 and 30 to 40 % PEG 400 at 12C.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→48.086 Å / Num. obs: 60826 / % possible obs: 99.96 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09956 / Net I/σ(I): 18.83
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.6858 / Num. unique obs: 5937 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WJ3

2wj3


Resolution: 2→48.086 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.42
RfactorNum. reflection% reflection
Rfree0.242 3007 4.94 %
Rwork0.1891 --
obs0.1917 60826 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 171.37 Å2 / Biso mean: 38.9548 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 2→48.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6203 0 39 602 6844
Biso mean--36.58 37.67 -
Num. residues----799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116397
X-RAY DIFFRACTIONf_angle_d1.0668711
X-RAY DIFFRACTIONf_chiral_restr0.06913
X-RAY DIFFRACTIONf_plane_restr0.0081159
X-RAY DIFFRACTIONf_dihedral_angle_d12.5473703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.03280.34941470.26592680
2.0328-2.06790.3221380.25482700
2.0679-2.10550.32281340.23352727
2.1055-2.1460.31141390.2352721
2.146-2.18980.2621420.2342705
2.1898-2.23740.3211470.22192717
2.2374-2.28940.30481380.21992725
2.2894-2.34670.25751280.21252722
2.3467-2.41010.25581320.2042729
2.4101-2.4810.27131290.20752718
2.481-2.56110.24921490.20222737
2.5611-2.65260.26841360.20232738
2.6526-2.75880.27471460.20622741
2.7588-2.88440.25671490.19522717
2.8844-3.03640.23711400.19632763
3.0364-3.22660.23361550.19082762
3.2266-3.47570.23861690.18832736
3.4757-3.82530.21131310.16892813
3.8253-4.37860.23511560.15742797
4.3786-5.51520.17831480.1442853
5.5152-48.10040.21641540.18513018

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