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- PDB-7tz9: Structure of PQS Response Protein PqsE(E182W) Variant -

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Basic information

Entry
Database: PDB / ID: 7tz9
TitleStructure of PQS Response Protein PqsE(E182W) Variant
ComponentsQuinolone signal response protein
KeywordsHYDROLASE / Quorum Sensing / PQS / PqsE / mutant
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / : / Quinolone signal response protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 Å
AuthorsJeffrey, P.D. / Taylor, I.R. / Bassler, B.L.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM134583 United States
National Science Foundation (NSF, United States)MCB-1713731 United States
CitationJournal: Biochemistry / Year: 2022
Title: The PqsE Active Site as a Target for Small Molecule Antimicrobial Agents against Pseudomonas aeruginosa.
Authors: Taylor, I.R. / Jeffrey, P.D. / Moustafa, D.A. / Goldberg, J.B. / Bassler, B.L.
History
DepositionFeb 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Quinolone signal response protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8013
Polymers34,6901
Non-polymers1122
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.028, 61.028, 146.717
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Quinolone signal response protein


Mass: 34689.668 Da / Num. of mol.: 1 / Mutation: E182W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: pqsE, PA14_51380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2Z6F6
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 15% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.01→29.34 Å / Num. obs: 21945 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Net I/σ(I): 19 / Num. measured all: 288714
Reflection shell

Diffraction-ID: 1 / % possible all: 97.2

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.01-2.0613.21.0562037015490.7380.3021.12.7
8.97-29.3410.60.031312529610.0090.03258.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.17_3644refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7KGX

7kgx


Resolution: 2.01→28.17 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 1152 5.26 %
Rwork0.1693 20744 -
obs0.1717 21896 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.8 Å2 / Biso mean: 48.2897 Å2 / Biso min: 22.29 Å2
Refinement stepCycle: final / Resolution: 2.01→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 2 109 2485
Biso mean--34.15 47.19 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062436
X-RAY DIFFRACTIONf_angle_d0.7873308
X-RAY DIFFRACTIONf_dihedral_angle_d18.749896
X-RAY DIFFRACTIONf_chiral_restr0.05357
X-RAY DIFFRACTIONf_plane_restr0.005430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.10.28071380.22542544268299
2.1-2.210.2451250.198625362661100
2.21-2.350.23731720.182725492721100
2.35-2.530.21591480.175125442692100
2.53-2.780.21191260.183126032729100
2.78-3.180.25121550.184225752730100
3.19-4.010.23081490.163726122761100
4.01-28.170.18011390.151227812920100
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)
15.7204-0.816-1.70853.1818-0.23223.14620.24970.70980.2848-0.16250.06390.1354-0.3762-0.1354-0.28670.32650.0208-0.00570.3034-0.03270.3289-25.8015-9.8723-27.8213
22.8725-0.104-0.05683.0065-0.79962.9614-0.13470.1854-0.3219-0.02160.05930.27010.0458-0.22570.06730.29990.0030.05160.2493-0.03510.3489-30.4696-11.8836-17.6685
32.9431-1.23260.26482.8874-0.2962.662-0.0061-0.1542-0.27390.33190.08780.3495-0.0692-0.4315-0.06670.29150.00560.05610.31710.03940.2867-33.0234-8.8316-13.0176
43.2949-0.01820.42692.1834-0.10471.9595-0.1019-1.1419-0.3260.75240.14060.16370.0281-0.2562-0.04820.56590.02580.08440.44570.04920.3066-29.7275-11.6077-2.9054
52.2439-0.53153.12791.3117-1.5529.3687-0.6408-0.78161.11031.19650.1061-0.106-2.0354-0.68890.29460.78360.09570.01560.5312-0.14390.4841-27.1763.5839-0.3224
63.7120.8244-1.02281.82271.79613.5125-0.1495-0.71790.23390.45730.05940.632-0.097-0.6260.09350.480.06780.02560.48880.02440.3586-31.8005-7.0573-4.1667
75.74531.82190.9213.69030.82842.1313-0.1033-0.0352-0.91130.05150.13140.21860.6380.0716-0.08890.53190.01690.00120.22150.05220.4589-21.3638-23.9699-13.7628
84.2792-1.0435-0.83811.2912-0.81243.37270.0942-0.2652-0.57770.57480.0269-0.0360.46030.0625-0.11090.32650.0352-0.0420.2330.02530.3003-16.2081-14.6581-12.306
93.06730.0417-1.13463.39491.76431.69560.1612-0.0780.26310.1787-0.1337-0.061-0.06820.218-0.05580.295-0.0028-0.04680.26770.02550.2937-13.2748-4.1814-18.161
101.51440.1685-0.83783.95751.89592.5960.11880.1923-0.12860.0444-0.0131-0.35060.19870.3706-0.07410.2670.0280.00090.23560.01570.2608-10.6621-11.482-19.3277
113.23233.73780.27655.27221.30210.9712-0.17740.05230.27010.10940.3833-0.0363-0.1620.4055-0.16560.3801-0.0588-0.0940.4442-0.03930.43470.23532.7847-16.5662
123.55040.9924-0.88252.3360.09492.06830.28730.281.6499-0.1862-0.27850.5943-0.6008-0.2897-0.04890.82510.0344-0.03660.4182-0.01630.8171-11.098711.5311-14.6187
136.273-2.97561.0235.2231-0.90933.63340.3878-0.88130.4666-0.1769-0.19840.1361-0.03040.3655-0.23390.6063-0.1205-0.00240.4655-0.14740.5078-5.94145.7605-6.0711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )A0 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 41 )A18 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 77 )A42 - 77
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 102 )A78 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 116 )A103 - 116
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 141 )A117 - 141
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 155 )A142 - 155
8X-RAY DIFFRACTION8chain 'A' and (resid 156 through 171 )A156 - 171
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 197 )A172 - 197
10X-RAY DIFFRACTION10chain 'A' and (resid 198 through 232 )A198 - 232
11X-RAY DIFFRACTION11chain 'A' and (resid 233 through 254 )A233 - 254
12X-RAY DIFFRACTION12chain 'A' and (resid 255 through 282 )A255 - 282
13X-RAY DIFFRACTION13chain 'A' and (resid 283 through 297 )A283 - 297

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