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- PDB-2q0j: Structure of Pseudomonas Quinolone Signal Response Protein PqsE -

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Basic information

Entry
Database: PDB / ID: 2q0j
TitleStructure of Pseudomonas Quinolone Signal Response Protein PqsE
ComponentsQuinolone signal response protein
KeywordsMETAL BINDING PROTEIN / quorum sensing / Pseudomonas Quinolone Signal / PQS / metall-beta-lactamase / iron / phosphodiesterase
Function / homology
Function and homology information


2-aminobenzoylacetyl-CoA thioesterase / secondary metabolite biosynthetic process / hydrolase activity / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / : / 2-aminobenzoylacetyl-CoA thioesterase / Quinolone signal response protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYu, S. / Jensen, V. / Feldmann, I. / Haussler, S. / Blankenfeldt, W.
CitationJournal: Biochemistry / Year: 2009
Title: Structure elucidation and preliminary assessment of hydrolase activity of PqsE, the Pseudomonas quinolone signal (PQS) response protein.
Authors: Yu, S. / Jensen, V. / Seeliger, J. / Feldmann, I. / Weber, S. / Schleicher, E. / Haussler, S. / Blankenfeldt, W.
History
DepositionMay 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Quinolone signal response protein
B: Quinolone signal response protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5118
Polymers73,0432
Non-polymers4686
Water6,774376
1
A: Quinolone signal response protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7554
Polymers36,5221
Non-polymers2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Quinolone signal response protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7554
Polymers36,5221
Non-polymers2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.760, 66.090, 110.260
Angle α, β, γ (deg.)90.00, 97.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Quinolone signal response protein


Mass: 36521.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cloned into NdeI/BamHI sites / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: pqsE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q02IG5, UniProt: P20581*PLUS
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM imidazole, 0.6 M NaAc, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→19.82 Å / Num. obs: 36642 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.976 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.73
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.6 / Num. measured obs: 14165 / Num. unique all: 4717 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.336 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS-REFINEMENT HAS BEEN USED THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1854 5.1 %RANDOM
Rwork0.151 ---
obs0.154 36641 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.76 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 22 376 5252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214991
X-RAY DIFFRACTIONr_bond_other_d00.023443
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9676779
X-RAY DIFFRACTIONr_angle_other_deg4.17538276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40222.48246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04415821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.311559
X-RAY DIFFRACTIONr_chiral_restr0.110.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025620
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021074
X-RAY DIFFRACTIONr_nbd_refined0.2360.21115
X-RAY DIFFRACTIONr_nbd_other0.260.23651
X-RAY DIFFRACTIONr_nbtor_refined0.180.22340
X-RAY DIFFRACTIONr_nbtor_other0.110.22527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2337
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5370.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3490.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.214
X-RAY DIFFRACTIONr_mcbond_it0.9011.53048
X-RAY DIFFRACTIONr_mcbond_other01.51239
X-RAY DIFFRACTIONr_mcangle_it1.5124844
X-RAY DIFFRACTIONr_scbond_it2.79831943
X-RAY DIFFRACTIONr_scangle_it4.0034.51935
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 140 -
Rwork0.161 2517 -
obs-2657 97.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.687-0.15260.04350.64110.19460.94320-0.0393-0.0288-0.0929-0.01050.09550.0109-0.09090.0104-0.056-0.01350.00460.00120.0027-0.059912.8492.19937.0219
20.7439-0.0979-0.1010.91540.00362.1341-0.073-0.1010.02490.19890.1205-0.0048-0.02970.0175-0.0476-0.05260.02630.02920.03740.0063-0.148124.98244.126349.0682
30.2596-0.04930.09980.39750.12940.62450.0007-0.0297-0.0286-0.0120.01680.08130.0009-0.032-0.0175-0.0672-0.02480.04160.00390.0179-0.067518.19062.285921.0519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-8 - 30112 - 321
2X-RAY DIFFRACTION2BB1 - 30121 - 321
3X-RAY DIFFRACTION3AI999 - 12291 - 231
4X-RAY DIFFRACTION3BJ999 - 11431 - 145

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