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- PDB-6et3: Crystal structure of PqsBC (C129S) mutant from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 6et3
TitleCrystal structure of PqsBC (C129S) mutant from Pseudomonas aeruginosa (crystal form 4)
Components
  • PqsB
  • PqsC
KeywordsTRANSFERASE / Pseudomonas Quinolone Signal / FabH / HHQ
Function / homology
Function and homology information


2-heptyl-4(1H)-quinolone synthase / secondary metabolite biosynthetic process / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / 2-heptyl-4(1H)-quinolone synthase subunit PqsC / 2-heptyl-4(1H)-quinolone synthase subunit PqsB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWitzgall, F. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2018
Title: The Alkylquinolone Repertoire of Pseudomonas aeruginosa is Linked to Structural Flexibility of the FabH-like 2-Heptyl-3-hydroxy-4(1H)-quinolone (PQS) Biosynthesis Enzyme PqsBC.
Authors: Witzgall, F. / Depke, T. / Hoffmann, M. / Empting, M. / Bronstrup, M. / Muller, R. / Blankenfeldt, W.
History
DepositionOct 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PqsC
B: PqsB
C: PqsC
D: PqsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,91812
Polymers138,1674
Non-polymers7518
Water9,224512
1
A: PqsC
B: PqsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6428
Polymers69,0842
Non-polymers5596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-45 kcal/mol
Surface area21980 Å2
MethodPISA
2
C: PqsC
D: PqsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2764
Polymers69,0842
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-49 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.184, 63.775, 119.131
Angle α, β, γ (deg.)90.000, 120.780, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 15 or resid 17...
21(chain C and (resid 1 through 2 or (resid 3...
12(chain B and (resid 1 through 15 or resid 17...
22(chain D and (resid 1 through 15 or resid 17...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETALAALA(chain A and (resid 1 through 15 or resid 17...AA1 - 154 - 18
121SERSERPROPRO(chain A and (resid 1 through 15 or resid 17...AA17 - 2920 - 32
131ASPASPASPASP(chain A and (resid 1 through 15 or resid 17...AA3033
141METMETCYSCYS(chain A and (resid 1 through 15 or resid 17...AA1 - 3484 - 351
151METMETCYSCYS(chain A and (resid 1 through 15 or resid 17...AA1 - 3484 - 351
161METMETCYSCYS(chain A and (resid 1 through 15 or resid 17...AA1 - 3484 - 351
171METMETCYSCYS(chain A and (resid 1 through 15 or resid 17...AA1 - 3484 - 351
211METMETHISHIS(chain C and (resid 1 through 2 or (resid 3...CC1 - 24 - 5
221LYSLYSLYSLYS(chain C and (resid 1 through 2 or (resid 3...CC36
231GLYGLYCYSCYS(chain C and (resid 1 through 2 or (resid 3...CC-2 - 3481 - 351
241GLYGLYCYSCYS(chain C and (resid 1 through 2 or (resid 3...CC-2 - 3481 - 351
251GLYGLYCYSCYS(chain C and (resid 1 through 2 or (resid 3...CC-2 - 3481 - 351
261GLYGLYCYSCYS(chain C and (resid 1 through 2 or (resid 3...CC-2 - 3481 - 351
271GLYGLYCYSCYS(chain C and (resid 1 through 2 or (resid 3...CC-2 - 3481 - 351
281GLYGLYCYSCYS(chain C and (resid 1 through 2 or (resid 3...CC-2 - 3481 - 351
112METMETVALVAL(chain B and (resid 1 through 15 or resid 17...BB1 - 151 - 15
122LEULEULEULEU(chain B and (resid 1 through 15 or resid 17...BB1717
132GLYGLYASPASP(chain B and (resid 1 through 15 or resid 17...BB19 - 3119 - 31
142METMETVALVAL(chain B and (resid 1 through 15 or resid 17...BB33 - 22333 - 223
152GLUGLUGLNGLN(chain B and (resid 1 through 15 or resid 17...BB225 - 251225 - 251
162ARGARGARGARG(chain B and (resid 1 through 15 or resid 17...BB252252
172METMETGLYGLY(chain B and (resid 1 through 15 or resid 17...BB1 - 2791 - 279
182METMETGLYGLY(chain B and (resid 1 through 15 or resid 17...BB1 - 2791 - 279
192METMETGLYGLY(chain B and (resid 1 through 15 or resid 17...BB1 - 2791 - 279
1102METMETGLYGLY(chain B and (resid 1 through 15 or resid 17...BB1 - 2791 - 279
1112METMETGLYGLY(chain B and (resid 1 through 15 or resid 17...BB1 - 2791 - 279
212METMETVALVAL(chain D and (resid 1 through 15 or resid 17...DD1 - 151 - 15
222LEULEULEULEU(chain D and (resid 1 through 15 or resid 17...DD1717
232GLYGLYASPASP(chain D and (resid 1 through 15 or resid 17...DD19 - 3119 - 31
242METMETVALVAL(chain D and (resid 1 through 15 or resid 17...DD33 - 5133 - 51
252LYSLYSLYSLYS(chain D and (resid 1 through 15 or resid 17...DD5252
262METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2811 - 281
272METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2811 - 281
282METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2811 - 281
292METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2811 - 281
2102METMETALAALA(chain D and (resid 1 through 15 or resid 17...DD1 - 2811 - 281

NCS ensembles :
ID
1
2

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Components

#1: Protein PqsC


Mass: 38551.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsC, PA0998 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X1
#2: Protein PqsB


Mass: 30531.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsB, PA0997 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris (pH 6.5), 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.211 Å / Num. obs: 63167 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.316.41.04144100.70.4451.134100
10.31-48.216.60.0297050.9990.0120.03299.1

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Processing

Software
NameVersionClassification
PHENIXdev_2875refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.22data extraction
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ET0

6et0


Resolution: 2.25→48.211 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.37
RfactorNum. reflection% reflection
Rfree0.2008 3061 4.85 %
Rwork0.1692 --
obs0.1708 63144 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.29 Å2 / Biso mean: 55.3049 Å2 / Biso min: 23.71 Å2
Refinement stepCycle: final / Resolution: 2.25→48.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9220 0 73 512 9805
Biso mean--85.44 45.65 -
Num. residues----1216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029560
X-RAY DIFFRACTIONf_angle_d0.54613022
X-RAY DIFFRACTIONf_chiral_restr0.0431463
X-RAY DIFFRACTIONf_plane_restr0.0031724
X-RAY DIFFRACTIONf_dihedral_angle_d12.3645796
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3373X-RAY DIFFRACTION8.196TORSIONAL
12C3373X-RAY DIFFRACTION8.196TORSIONAL
21B3030X-RAY DIFFRACTION8.196TORSIONAL
22D3030X-RAY DIFFRACTION8.196TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.28520.28751550.260227142869
2.2852-2.32260.25011320.24526892821
2.3226-2.36270.26681560.249227092865
2.3627-2.40560.27771280.238526672795
2.4056-2.45190.32991380.248927742912
2.4519-2.5020.27631550.240226882843
2.502-2.55640.27531520.223127022854
2.5564-2.61580.23261270.205126902817
2.6158-2.68120.21371310.193227402871
2.6812-2.75370.23351410.201827442885
2.7537-2.83470.21451300.187826952825
2.8347-2.92620.21721510.193527202871
2.9262-3.03080.27941140.192727462860
3.0308-3.15210.22211320.189827282860
3.1521-3.29550.22761200.166927382858
3.2955-3.46930.17351500.155627382888
3.4693-3.68650.14081480.144627252873
3.6865-3.97110.16541370.134227542891
3.9711-4.37040.1641310.120927342865
4.3704-5.00230.14891570.120427652922
5.0023-6.30010.19991470.15727662913
6.3001-48.22160.20011290.178928572986
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)
12.615-0.48820.83772.54540.70732.62210.3493-0.2018-0.03090.6985-0.1115-0.39570.7281-0.129-0.27910.648-0.1312-0.05170.34870.10080.3308184.8718-21.96847.2104
24.48440.34410.66462.94110.44862.27640.29510.0519-0.5320.1948-0.2776-0.09310.7831-0.08560.0140.5425-0.0718-0.03360.270.00310.3346180.8302-29.377-12.8107
36.3844-1.62710.61077.815839.4902-0.004-0.0450.0994-0.0188-0.10730.19230.0375-0.51910.07570.3307-0.12190.03530.3153-0.00660.238168.2795-20.7385-10.9217
45.2915-1.06883.04240.42820.04513.96720.1655-0.00790.12150.1229-0.1969-0.00740.393-0.16020.04250.4453-0.12220.0040.31020.02080.3011178.863-22.0452-4.332
55.84151.58694.57681.98911.6556.8239-0.0683-0.54490.42020.0026-0.54840.0779-0.2224-1.38830.55440.40470.00060.09581.0162-0.13110.4865163.2603-14.03690.7365
63.645-0.74890.55582.76971.02723.1378-0.0605-0.63080.2080.6042-0.29530.25590.4035-1.16350.31980.6252-0.2710.03210.781-0.09640.3571168.9361-17.2059.6666
71.7367-2.36351.30854.2278-0.77211.9262-0.0912-0.6354-0.32160.6593-0.28970.3990.6082-1.83530.00140.7495-0.43350.18771.0081-0.06470.4175164.59-23.04834.5942
82.92360.579-1.28382.0617-0.09852.9030.2357-0.19560.42650.3487-0.17730.2465-0.4927-0.2759-0.05980.39010.0230.00830.3841-0.10350.3247174.3272-3.6723-20.575
94.81340.55230.05212.02420.01582.46740.02230.2684-0.1277-0.0668-0.06870.1042-0.0211-0.36620.04920.2641-0.0115-0.01080.3186-0.0550.2208174.3995-13.8427-31.634
101.8680.8158-2.28441.343-1.4864.9064-0.06560.10340.1015-0.26460.06730.1-0.1297-0.1874-0.08910.3780.059-0.0710.42570.07960.4102179.729319.468724.5974
114.80683.7122-3.91744.2637-2.58633.6363-0.74571.681-0.0397-0.40510.50570.13120.3531-0.8480.19860.572-0.0603-0.01490.69670.00610.3923186.061816.34794.8189
121.78260.9981-0.7240.7298-0.74783.03970.1365-0.03940.2720.0315-0.03360.0756-0.5378-0.0932-0.1150.36760.0475-0.00560.2074-0.01090.2973187.68318.660835.34
133.25611.5065-2.90980.6571-1.84835.9425-0.175-0.0853-0.1728-0.3193-0.1107-0.01470.07410.17560.38130.33230.03980.00310.21560.02540.3263187.991215.072524.2075
142.64960.5182-0.70311.2009-0.11481.94470.02470.12620.0336-0.1002-0.01990.1503-0.0942-0.2477-0.01520.32440.0395-0.08390.27540.03830.2475181.6666.391628.4493
156.79120.0662.70296.93963.78067.5592-0.24850.7722-0.0719-0.44480.0007-0.2811-0.279-0.15510.20110.55560.00360.06340.46230.05470.2897201.536811.235411.2442
168.33-3.8516-7.45642.78983.45398.40350.3030.5085-0.5169-0.4142-0.4484-0.1744-0.4176-0.00490.11840.4401-0.0607-0.13280.59790.02290.4277176.3866-1.883518.6282
172.46890.3665-1.43662.1762-0.61143.65650.15950.42390.043-0.23670.08160.293-0.0399-0.8345-0.22290.43110.0975-0.12240.54630.0710.3933171.403211.170718.2498
183.5694-1.1837-0.11012.88210.02311.81580.22120.09180.0817-0.1877-0.04480.5671-0.31-0.7677-0.16320.34990.0998-0.05470.54260.06380.372170.220611.436227.1394
194.43172.9653-4.13852.8469-2.19714.70410.3924-0.3569-0.7065-0.0573-0.3358-0.18670.08150.3025-0.04530.35040.04-0.03010.31790.02430.3939204.8181-6.971741.2894
202.7686-2.6103-3.12856.95622.77813.59070.029-0.31930.0315-0.13130.0432-0.28310.01650.7274-0.00230.22870.0247-0.00920.36630.02360.3054214.30771.279337.6215
215.13236.9173-5.21469.3309-7.01495.3091-0.1988-0.1027-1.0425-0.1584-0.055-0.46540.89760.310.3440.46150.0341-0.02340.299-0.00250.4656199.1854-12.80233.675
225.23231.9443-1.2071.1871-1.4153.91680.06050.3292-0.388-0.14360.0162-0.05990.31590.0373-0.05890.32090.0452-0.06290.2288-0.00660.33195.7669-4.014927.5098
233.6962-2.2897-1.36251.8284-0.2285.9208-0.1019-0.0971-0.1129-0.0882-0.05280.3542-0.0527-0.23570.1140.2052-0.0059-0.05650.16540.04340.2434186.3739-0.368237.5901
244.1445-0.41190.82260.0148-0.13213.8406-0.09670.0972-0.0751-0.02640.0592-0.05950.02790.57260.04430.27410.04250.01530.23050.00470.2968202.64931.954436.98
255.00781.615-0.07942.97161.14574.63610.1217-0.50860.26380.1707-0.12660.1744-0.1813-0.00040.0170.16260.0563-0.04260.23140.05640.1734195.04316.013348.9306
262.9973-0.02521.61942.36710.53026.08440.34730.05420.2484-0.29880.0699-0.1441-0.83671.0444-0.3870.3236-0.11480.03480.3651-0.01140.3483210.523114.256431.4758
273.45480.5248-2.57352.31720.4512.66320.0621-0.8009-0.18430.31840.0315-0.30750.20230.5936-0.0850.3896-0.0103-0.07890.55690.03980.3122203.29922.160954.5275
285.34871.212-2.84675.1483-4.66788.4631-0.2586-0.34-0.6564-0.0210.0624-0.1810.56910.23750.1930.2405-0.0336-0.05240.30380.04910.2998198.1409-6.822150.7611
295.91284.2636-1.18185.09340.57666.26880.0524-0.1927-0.15480.219-0.00850.05680.34180.1673-0.08090.16920.0506-0.04660.32060.02120.2337194.2471-0.886748.9548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )A1 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 115 )A46 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 144 )A116 - 144
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 184 )A145 - 184
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 242 )A185 - 242
6X-RAY DIFFRACTION6chain 'A' and (resid 243 through 314 )A243 - 314
7X-RAY DIFFRACTION7chain 'A' and (resid 315 through 348 )A315 - 348
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 132 )B1 - 132
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 279 )B133 - 279
10X-RAY DIFFRACTION10chain 'C' and (resid -2 through 25 )C-2 - 25
11X-RAY DIFFRACTION11chain 'C' and (resid 26 through 45 )C26 - 45
12X-RAY DIFFRACTION12chain 'C' and (resid 46 through 144 )C46 - 144
13X-RAY DIFFRACTION13chain 'C' and (resid 145 through 175 )C145 - 175
14X-RAY DIFFRACTION14chain 'C' and (resid 176 through 212 )C176 - 212
15X-RAY DIFFRACTION15chain 'C' and (resid 213 through 232 )C213 - 232
16X-RAY DIFFRACTION16chain 'C' and (resid 233 through 256 )C233 - 256
17X-RAY DIFFRACTION17chain 'C' and (resid 257 through 314 )C257 - 314
18X-RAY DIFFRACTION18chain 'C' and (resid 315 through 348 )C315 - 348
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 17 )D1 - 17
20X-RAY DIFFRACTION20chain 'D' and (resid 18 through 33 )D18 - 33
21X-RAY DIFFRACTION21chain 'D' and (resid 34 through 49 )D34 - 49
22X-RAY DIFFRACTION22chain 'D' and (resid 50 through 88 )D50 - 88
23X-RAY DIFFRACTION23chain 'D' and (resid 89 through 117 )D89 - 117
24X-RAY DIFFRACTION24chain 'D' and (resid 118 through 145 )D118 - 145
25X-RAY DIFFRACTION25chain 'D' and (resid 146 through 176 )D146 - 176
26X-RAY DIFFRACTION26chain 'D' and (resid 177 through 201 )D177 - 201
27X-RAY DIFFRACTION27chain 'D' and (resid 202 through 238 )D202 - 238
28X-RAY DIFFRACTION28chain 'D' and (resid 239 through 264 )D239 - 264
29X-RAY DIFFRACTION29chain 'D' and (resid 265 through 281 )D265 - 281

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