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- PDB-3dh8: Structure of Pseudomonas Quinolone Signal Response Protein PqsE -

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Basic information

Entry
Database: PDB / ID: 3dh8
TitleStructure of Pseudomonas Quinolone Signal Response Protein PqsE
ComponentsUncharacterized protein PA1000
KeywordsMETAL BINDING PROTEIN / QUORUM SENSING / PSEUDOMONAS QUINOLONE SIGNAL / PQS / METAL-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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
bis(4-nitrophenyl) hydrogen phosphate / : / 2-aminobenzoylacetyl-CoA thioesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement of native structure 2q0i in REFMAC5 / Resolution: 1.8 Å
AuthorsYu, 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
DepositionJun 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein PA1000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9694
Polymers34,5171
Non-polymers4523
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.980, 60.980, 146.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Uncharacterized protein PA1000 / Pseudomonas Quinolone Signal Response Protein / PqsE


Mass: 34517.484 Da / Num. of mol.: 1 / Mutation: E182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1000 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P20581
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-B4N / bis(4-nitrophenyl) hydrogen phosphate


Mass: 340.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 46.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 100mM HEPES, 200mM MgCl2, 30% PEG 400, 5mM bis-pNPP, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97881 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 2, 2008
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 30154 / Num. obs: 30110 / % possible obs: 99.8 % / Observed criterion σ(I): 4.3 / Redundancy: 11 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.3 / Num. unique all: 4432 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: Rigid body refinement of native structure 2q0i in REFMAC5
Starting model: 2Q0I

2q0i


Resolution: 1.8→19.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.654 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS refinement was used throughout (1 TLS body including all atoms), restraints for bis-pNPP were generated with PRODRG
RfactorNum. reflection% reflectionSelection details
Rfree0.19627 1495 5 %RANDOM
Rwork0.15608 ---
obs0.15809 28614 99.95 %-
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: 25.648 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 25 224 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0212497
X-RAY DIFFRACTIONr_bond_other_d0.0020.021716
X-RAY DIFFRACTIONr_angle_refined_deg2.2071.9713403
X-RAY DIFFRACTIONr_angle_other_deg1.1393.0014120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10922.48125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9731530
X-RAY DIFFRACTIONr_chiral_restr0.1550.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
X-RAY DIFFRACTIONr_nbd_refined0.2320.2513
X-RAY DIFFRACTIONr_nbd_other0.2230.21878
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21201
X-RAY DIFFRACTIONr_nbtor_other0.0930.21394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2183
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3890.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3630.27
X-RAY DIFFRACTIONr_mcbond_it1.9311.51642
X-RAY DIFFRACTIONr_mcbond_other0.4981.5612
X-RAY DIFFRACTIONr_mcangle_it2.27522401
X-RAY DIFFRACTIONr_scbond_it3.84631099
X-RAY DIFFRACTIONr_scangle_it5.394.5996
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 117 -
Rwork0.16 2071 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: -20.0979 Å / Origin y: -6.2855 Å / Origin z: -13.445 Å
111213212223313233
T-0.0156 Å20.0349 Å2-0.0322 Å2--0.1287 Å20.0015 Å2---0.0892 Å2
L2.1171 °2-0.0532 °2-0.165 °2-1.171 °20.1336 °2--1.4574 °2
S-0.0546 Å °-0.1571 Å °0.0141 Å °0.2273 Å °0.0476 Å °-0.0041 Å °-0.0628 Å °-0.009 Å °0.0071 Å °

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