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- PDB-6ra2: Structural basis for recognition and ring-cleavage of the Pseudom... -

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Basic information

Entry
Database: PDB / ID: 6ra2
TitleStructural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC
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 / Alpha/beta hydrolase fold-1 / 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
Dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase) / 2-heptyl-3-hydroxy-4(1H)-quinolone dioxygenase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 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 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_symm_contact / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_sheet_range
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_symm_contact.auth_seq_id_1 / _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_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_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

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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)


Theoretical massNumber of molelcules
Total (without water)89,3933
Polymers89,3933
Non-polymers00
Water10,142563
1
A: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)


Theoretical massNumber of molelcules
Total (without water)29,7981
Polymers29,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)


Theoretical massNumber of molelcules
Total (without water)29,7981
Polymers29,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)


Theoretical massNumber of molelcules
Total (without water)29,7981
Polymers29,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.816, 96.816, 189.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-443-

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 (bacteria) / Gene: MAB_0303 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MFK2, UniProt: A0A1M8M580*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
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.
PH range: 6.2-6.8

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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→46.91 Å / Num. obs: 40361 / % possible obs: 99.3 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06186 / Net I/σ(I): 29.82
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.1996 / Num. unique obs: 3990 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WJ3

2wj3


Resolution: 2.3→46.907 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 3.2 / Phase error: 24.2
RfactorNum. reflection% reflection
Rfree0.2482 2031 5 %
Rwork0.1853 --
obs0.1884 40631 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6154 0 0 563 6717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076327
X-RAY DIFFRACTIONf_angle_d0.8678615
X-RAY DIFFRACTIONf_dihedral_angle_d3.3613661
X-RAY DIFFRACTIONf_chiral_restr0.053904
X-RAY DIFFRACTIONf_plane_restr0.0071145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.35360.28971340.20222531X-RAY DIFFRACTION100
2.3536-2.41240.2981320.20182540X-RAY DIFFRACTION100
2.4124-2.47760.31261280.2022556X-RAY DIFFRACTION100
2.4776-2.55050.25121280.20492555X-RAY DIFFRACTION100
2.5505-2.63290.30251390.20032546X-RAY DIFFRACTION100
2.6329-2.72690.2611370.21082529X-RAY DIFFRACTION100
2.7269-2.83610.29661430.21152553X-RAY DIFFRACTION100
2.8361-2.96520.30121380.21372557X-RAY DIFFRACTION100
2.9652-3.12150.29851350.20732579X-RAY DIFFRACTION100
3.1215-3.3170.25161390.20712534X-RAY DIFFRACTION100
3.317-3.5730.2671320.18722590X-RAY DIFFRACTION99
3.573-3.93240.21971450.17162569X-RAY DIFFRACTION99
3.9324-4.5010.19551200.16072613X-RAY DIFFRACTION99
4.501-5.66930.20731410.15532617X-RAY DIFFRACTION98
5.6693-46.91660.2231400.17612731X-RAY DIFFRACTION97

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