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- PDB-6rb3: Structural basis for recognition and ring-cleavage of the Pseudom... -

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Basic information

Entry
Database: PDB / ID: 6rb3
TitleStructural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqdC variant in complex with its substrate
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


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / 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-heptylquinoline-3,4-diol / Dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase) / 2-heptyl-3-hydroxy-4(1H)-quinolone dioxygenase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 9, 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 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_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif / 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_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _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
E: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
A: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
B: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0186
Polymers89,2403
Non-polymers7783
Water8,071448
1
E: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0062
Polymers29,7471
Non-polymers2591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0062
Polymers29,7471
Non-polymers2591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0062
Polymers29,7471
Non-polymers2591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.644, 96.644, 190.138
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-546-

HOH

21B-525-

HOH

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Components

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


Mass: 29746.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: MAB_0303 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MFK2, UniProt: A0A1M8M580*PLUS
#2: Chemical ChemComp-JWW / 2-heptylquinoline-3,4-diol


Mass: 259.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H21NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M tri sodium citrate pH 5.6 and 30% PEG 4000

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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 / 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: 2.3→47.535 Å / Num. obs: 40828 / % possible obs: 99.97 % / Redundancy: 2 % / Biso Wilson estimate: 31.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04034 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.1891 / Num. unique obs: 3981 / CC1/2: 0.905

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RA2

6ra2


Resolution: 2.3→47.535 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2456 2078 5.09 %
Rwork0.1952 --
obs0.1978 40828 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.42 Å2 / Biso mean: 41.331 Å2 / Biso min: 17.8 Å2
Refinement stepCycle: final / Resolution: 2.3→47.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6222 0 117 448 6787
Biso mean--65.89 37.41 -
Num. residues----801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.35350.27021190.215725492668
2.3535-2.41240.26171370.209825232660
2.4124-2.47760.281290.204925542683
2.4776-2.55050.29251170.220225492666
2.5505-2.63280.29081350.214425492684
2.6328-2.72690.27091360.216725362672
2.7269-2.83610.27261500.21725582708
2.8361-2.96520.24581420.199625392681
2.9652-3.12150.25431230.209325892712
3.1215-3.3170.25631460.214525642710
3.317-3.5730.29031360.208625842720
3.573-3.93240.2171440.180725902734
3.9324-4.50110.21661270.165326392766
4.5011-5.66940.20651540.159826492803
5.6694-47.54460.23311830.201527782961

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